I'm on a Mac; I've always played this game via the app (it's usually just - easier on Macs in general to download that way), but this was my first time doing an update. Still: I've never had any issues with updating other games, hence me being so freakin Confused. The only thing I can think of... maybe because I didn't do the last update? (I wanted to wait for one of the main girls' content before diving back in) But - that would be stupid, if that's the reason....
I'll do some digging around tomorrow and see if I can uncover some save files or roll back the update or - SOMETHING; put my Millennial to the test. If all that fails - I mean: there's nothing I can do - I'll have to play it from the beginning. Which will really suck, but... I guess I'll just wait for you to be finished with the entire game and then do it. I couldn't bear this happening to me again. Thanks for caring, regardless - you're awesome.
Like I said I don't know about the itch app, but I might be able to help a little bit.
Renpy saves on Mac are supposed to be stored in $HOME/Library/RenPy/ and then a Yuri University folder. If the app uses the same file type, which I assume it does, at the very least I could either help you reconstruct your lost save, or even just give you a little boost to speed through the early game easier.
I won't finish making the game for at least a year, so that would be a big wait, but totally understand 😥