TLDR: Just did some testing with it and it seems the legendary netrunner cyberdecks are causing this.
I have the same issues
- no rare/uncommon crafting specs after getting the two lower perks (Hackers Manual and advanced)
- epics/legendar blueprints disappear after crafting
I have the legendary Netwatch MK5 installed.
So i went back to an earlier save where I only had the legendary Raven MK4 installed.
After getting the two lower perks, I had the uncommon/rare blueprints in my crafting menue.
However, they disappeared after crafting.
I reloaded the game again, went to a ripperdock and purchased the legendary Arasaka
After getting Hacker's Manual i noticed that 2 uncommon blueprints where missing: ping and cyberware malfunction.
Well, I assume the Netwatch cyberdeck just gets rid of all uncommon/rare ones.
IMHO this is not a huge deal because uncommon und rare are pretty common to buy from netrunner shops.
The fact the epics/legendaries disappear is not a problem because once you have them you can't lose them.
But yeah, it's annoying AF when you don't know why they are missing.
Hope that helps.
Cheers, Lia