Sounds like something going on with the files themselves or something getting confused trying to sync them. Do you have a program like OneDrive attempting to back up the files in your My Documents folder? I remember other people having an issue regarding that.
What I would do is load the game up again, drop a hard save. Then exit out and cut and paste all other saves and auto saves to a backup folder. Then launch the game from the one save, play as normal, and see if your future saves work after that. I'd also disable any steam cloud sync, larian sync, or one drive syncing to test if that's an issue too.
I don't back my files to OneDrive or any other drive like that, everything is on my computer and steam cloud (as to Larian sync, I am not sure if it's on so I'll make sure to check)
As to what you suggested, I think I'll try it and we'll see. I also thought about clearing everything including character profiles and then trying to make a brand new character to test if it works.