That's a bunch of work for nothing. Basically, with a redownloaded game and redownloaded patch, I started up the Fate route, quickly finished that and quit the game. - Only from then on I couldn't start any of the routes anymore unless I deleted the saved files in my savedata folder.
Tried to start UBW from a clean savedata and made some saves, quit the game and tried to reopen with the same error.
So, I copied my old savedata backup back in again and was able to start and exit the games on a whim like normal, so something must be wrong with the new patch files I downloaded?
The backup savedata folder was made after completing the Fate route though, so I can start UBW without corrupted saves (that are impossible to delete) - only every time I do that now, I get corrupted saves in UBW anytime, doesn't matter when I save. It's impossible to progress properly.
I'm really lost. Maybe I'll try a second redownload of everything tomorrow.