First of... sorry for the long post... it's just in my nature, and no matter how much I try, and how much time I spend on "making my posts smaller" (and believe me, it often takes me more time fixing a post, then actually writing it the firs time... XD ), they still almost always end up being at least big, if not huge. XD
But, if you stick with me to the end, you might potentially find a solution that works for your problems, just like it did for me when I started investigating this bugged mission in my Journal.
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Anyway... I also have this bug, where even though I finished the Troublesome Neighbors mission it was never moved to the Completed section of the Journal. But... I have managed to successfully fix this mission for me (getting the mission to be moved fram the "active" part of the Journal, to the Completed section of the Journal)... with potentially only one small snag left, which I do not know if it will come back to bite me later on or not. XD
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An important note to make here.
The way I finished this mission, when I encountered it days ago (I think I found, played, and finished this mission anywhere from 4-7'ish days ago, and that is out of 9, closing on 10, days playing the game), was to take the target alive. I took care of her guards, and then I snuck up on her, choked her out, and then carried her out and dump her in the trunk of a car that the mission supply you with, and then the car drives away by it's self and the mission ends leaving you there on the street.
The other way to finish it is by simply killing the target, and from what I have seen on youtube that ends the mission right then and there (no carrying the target to a car or anything, don't think the car even shows up if you kill her).
This is important to note because so far, in my "investigation" that I have done with this mission, all the people I have seen who talk about having this bug (and also mentioning how they finished the mission) all say that they took her alive and dumped her in the trunk of a car. It seems like no one who killed the target has gotten this bug, at least based on what I have seen from other people mentioning this bug on this mission. I could still be wrong about this of course, but this is what the pattern is showing me right now.
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This here below is what worked for me (combined with additional suggestions that I feel can be useful after I spent the time with it).
But first... so some of you do not potentially waste your time trying this. If you have finished all of Reginas missions at this point in time, and you do not have any older saves from befor finishing all her missions, then I do not think you can go any further then this... because the fix I found relies on finding a new mission from Regina out in the world. If that is not possible for you anymore, then this can not, or is at the very least extremely unlikely to help you fix this bug for you. But maybe you figure something out by reading my findings and suggestions that could help you, who knows.
So... the steps to do the fix I found. This all takes place in the game, there is no modding of any files or anything, just plain and simple playing the games and trying a set of steps and actions in the game to try and force the game to do what it is supposed to do with the mission.
Nr 1 - Pick the save you want to try this on, a save where the mission is bugged and has not moved to the Completed section in the Journal. Load that save up, and then just to be safe make a new manual save and use that one when trying thing. Do that for each new save you try. It's not necessary, but if anything you keep your original save files safe, who know when you suddenly by accident pick "save" one time instead of "load" you know. XD
Nr 2 - For each new save you try, get your self over to where the mission "Troublesome Neighbors" takes place, you need to check something there. I have an image of the map ("Map_1_Kabuki") and minimap ("RD_2") that you can check, those images show you the area you need to go to.
In both the large map, and in the minimap image, (and the scanning image, "RD_1") my character is standing in the same location in the world, which is on the side walk just outside the entrance/exit you are lead to when leaving the building carrying the target, and in front of the street you are lead to where you need to put the target in a cars trunk. I find that the quickest way to get there is to fast travel to either the blue marker to the south, or the north, of the mission area, and then running the rest of the way.
What you should check for here is the small street that my character is standing on/by, by the entrance/exit I mentioned above. This is the street location where the car spawn that you put the target in the trunk of the car. What you need to specifically check for though is the actual driver. For me he was standing in the street, so no car or anything, just standing there in the middle of the street impeding traffic. Check Map_1_Kabuki and RD_2 for the street and location, and check the image of RD_1 for what he looked like for me, at least through the scanner. I don't know if it is always a he, or if the Driver always looks the same for everyone, could be random... so the best way to identify the Driver is by the fact that he has a green circle on the minimap, and when you get close enough a green text of "Driver" shows up above their head, scanning them also says that they are "Regina's Driver" like the RD_1 image shows.
So... If the Driver is not present in this location, then you should have a save where the fix I found might just work (it of course depends on your circumstances). I think each save file I checked, where there was no driver on the street, and where I tried the fix on, it worked almost every time. There does seem to be maybe some level or randomness to it, but if so it is minimal in my experience... or I just remembered it incorrectly, or did something wrong that changed something for that particular try.
Now, if there actually is a Driver present on that street, then that should change some things (which it did for me) with what you might see happen when doing the next step in this process. I also noticed that the chance of my "fix" working with each save with the Driver is either 0, where it never works for that particular save file ever... or it seems a bit low and random for the other save files with the Driver.
Now the save file I decided to finally use, to fix my games bugged "Troublesome Neighbors" mission, actually had the driver on that street... and even now, after the mission has been fixed, the driver is still there. But after that save randomly worked for me, I felt this save was the one that would lose me the least game time played, since all the save files without the driver was older then this one. This is also why I at the start mentioned that even though I had fixed my bugged mission, there was a snag that I do not know if it will come back to bite me later or not. That snag being that the Driver is still there on the street in the area next to where Troublesome Neighbors took place... so if he is needed at a later time he might not be available due to that, or he might just teleport from that street to where he needs to be... I don't know. XD
Nr 3 - You need to find a new mission from Regina (the Fixer that gave you Troublesome Neighbors), a mission which you have not encountered befor at that point in time of that save. It can still be a mission that you can see the yellow circle with the ! in it on the map on beforehand, you must just never have been close enough to it befor where it triggered for you (if that was the case though, you would see it in your Journal with name and everything). I don't think it can be a "buy car" mission though, I think it needs to be one of the "normal" missions... or at least I assume this is the case, because I never checked.
This might be difficult and/or time consuming if you do not know where any of Reginas mission might be on the map, which means you just have to drive around all over, and sometimes get out of you car as well to check things (as I will mentions soon below). Because you need to be close enough to them so that Regina would trigger those missions for you and talk to you about it over the phone. But finding them might be made more difficult by the fact that some mission seems to be able to be trigger when you are both in and outside of the car when you get close... where as other missions only seem to trigger when you are outside of your car, these ones are especially hard to find I would asume if you do not look up some guide or something.
I got lucky when I found the mission I ended up trying out all my theories for Troublesome Neighbors on. Because the mission I found seemed to need you to step outside of your car, and I just so happened to do that in the area of that new Regina mission, because something interesting happened right in front of me and I stepped out of my car to check it out. As soon as I did Regina instantly called me, and started to tell me about Troublesome Neighbors, and then directly after talking to me about this new mission I had found... which seemed to prove my theory that you needed a new Regina mission to trigger to trigger the Troublesome call again. Sometimes though she only started talking about the new mission as I was leaving the area, either in or outside of the car... was a bit random... but without fail, each time I went to that new mission, the Troublesome mission would trigger and trigger first as well. So I had found my location to try and find a fix for the bugged mission.
The mission that I ended up using to test my experiments on (I would load save file after save file , and reload others over and over to try different things, etc, and constantly make that run to that same mission each time), and ultimately the mission that I used the entire time, and that helped fix Troublesome for me, is a mission called "Cyberpsycho Sighting: Six Feet Under" (check the image "Map_2_Northside for location).
I already had that icon on the map since a long time ago, and all I knew about it was that it was a "Side Job"... it is not until I happen to step out of my car that it reveled it's self to be a Regina missions.
Nr 4 - When you have found a, or a few, new Regina missions... then start to go to this/these new Regina missions with the save files you want to try. Remember that when you get there you might have to step out of your car for the whole thing to trigger, but you might not have to if it still triggers when you are in the car. I would though still leave the car anyway, just to remove one potential snag in the equation. I would also suggest that you use the fast travel mechanics in the game to get close to the new missions, call in your car, and drive the last bit, just to cut down on time. But if one of these new Regina missions are very close to the fast travel location (like so close that it could trigger the mission by just fast traveling there), then I would maybe try it a few times that way, but then also pick a fast travel location that is a little bit further away... just to see if there is a difference with triggering it all via the car, stepping out of the car, or fast traveling.
When she triggers the new mission she should instantly trigger Troublesome Neighbors as well which then should takes nr 1 priority and goes befor anything else, even the new mission you triggered. When this happen, and this is maybe very important, do not answer her call by pressing the key you have assigned to answer calls (T by default I think)... just let the ring signal continue to ring out unanswered. If you let the ring signal go long enough the game will automatically answer the call by it's self for you... just let the game do that. Also, through out this entire process starting with the first call, let every call and message that you receive there go by them selves, just let them show up and then hang up by them selves and/or fade away all by them selves.
The reason I say this is not because I know this makes a difference, I say this because I feel it will remove any possible effect you your self might have on the game/process by pressing a key to answer the call/message, and because one of the theory I have is that maybe pressing the key to answer one to many calls to quickly could maybe be the cause of the original mission bugging as soon as it was done (because after that I was bombarded with maybe 3 calls one after another, plus a bunch of text messages and game messages about mission being finished etc). And as such, just leaving the games own default process to deal with it, and not actually check any of it untill it is all done, seems like a good thing to do.
Now if this worked for you, and things go as they should, as the calls come and go, and as the various messages come and go, at some point in here the game should inform you that the mission Troublesome Neighbors was finished (just like it did back when you actually played and finished the mission befor)... but if you are lucky, this time the game will have actually moved the mission to the Completed section of the Journal. Do not check this until all the calls and messages etc are done, just to make sure... and if things went as they did for most of my successful tries, then the mission should by this point have been moved to where it is supposed to be.
Now... for some added information... there are two different scenarios, with two different endings for each scenario here, for a total of 4 different combinations of outcomes. Two where the mission was moved in the Journal and the bug was fixed, and 2 where the mission did not move and the bug persisted. The different scenarios here depends on if the Driver exist at the bugged missions area or not.
If there is no driver at the bugged missions area, then when you reach the new missions area Regina will call you and ask you to check out the bugged mission and take care of the target and all... and as you let the messages come and go by them selves until they all end this will eventually lead to the bugged mission finishing again, and then either be moved in the Journal to Completed and the bug is fixed, or the mission was finished again but is not moved and the bug persists.
Now if there is a driver in the bugged missions area, then when you reach the new mission area the same thing will happen as when there was no driver in the bugged missions area... except for one thing. Regina will call you about the Troublesome Neighbors mission like befor, but she will not ask you to go check the mission and and deal with the target... what she instead does is call you about you finishing the mission, where she says something along the lines of that it was unusual that you took the target alive instead of just killing her. Now the outcome of this is the same as befor, either the bugged mission moved in the Journal and the bug is fixed, or the mission did not move and the bug persists.
This is at least what I saw in my saves... that the call I got from Regina was different depending on if the driver existed at the bugged missions mission area.
The chances of these things though, at least for me and my certain set of circumstances, if the bug was fixed or not at the end of each try, depended on if the Driver was in the bugged missions area or not. No driver, then the chances where very high that the bug was fixed for me... but if there is a driver then the chance that the bug was fixed for me is either very low, or none existence and will always fail (due to that part about some saves with the Driver would fail to move the bugged mission every single time for me, but where some saves with the driver would move the bugged mission and fix the bugs on a few occasions).
In the end, all you have to do is try each save a few to several times, to see what happens. And if it is not working, then maybe try to find another new Regina mission to see if that works instead. Another thing that also might work, but which I am not sure if it does at all since I never had to try it... is to instead of just going to one new mission to let this happen, go to 2 or more new Regina missions in a row, seeing if the bugged mission triggers each time or not, or only triggers on every other or third or what ever new mission you reach, and seeing if you get the "mission finished" each time or not, and finally checking the Journal each time to see if the bugged mission was moved to the right place and fixed or not.
Nr 5 - "Nr 5?! Have you not talked long enough by now!?" you might ask... XD Yes... soon... I just wanted to add that from now on I would continue to never my self answer the calls, or the messages, and any other "press that key to follow/read/etc this mission"... because while they might seem convenient, to not have to go into the menus every single time to find the new stuff, currently there still remains the thought that these kinds of bugs might just have happened because the system was overloaded with to many messages and to many key presses to respond to each one of them. For not it is an uncertainty... so for me I will stay away from them, not that I used to respond a lot do these messages with pressing the suggested key... other then T for answering actual calls. But since I figured out that the calls will be answered by them selves eventually, I will just let the game do that from now on... if anything it gives me time to stop what I am doing, brake in for a full stop with my vehicle (most vehicles seem to need an entire runway to break to a full stop... XD ), and prepare my self for taking in the information they are trying to give me. XD
I think that is all I can say about all this... and I have said a hell of a lot by now, for which I am sorry... but hopefully it has been at least helpful, even if you all just skimmed through 95% of the entire thing trying to get to the core nuggets of it all. XD