Well, for me, even if I try to launch the game without admin rights or compatibility mode, still it works fine for me and the save file is working just fine. Try to check if you are logged into admin account and not on any restricted account.
Do not worry, there is a complete quests of individual save game file that you can download from this link - http://goo.gl/j8konx
Just copy and paste from any save game file quests that you want and play from that quests directly.
Yes, thats the correct location for the GOG version but for Steam the save game location is different. Additionally, you can also download The Witcher 3 Wild Hunt save game for PC from this link - http://goo.gl/j8konx
Yes, this would be a great idea. However you can also keep save game for individual quests as a backup. If you want then you can also get this individual quests save game files of Wither 3 from this link - http://goo.gl/j8konx