Hey there, sorry for the delay in getting back to you. It's not perfect, but we might have a solution for you:
Our best guess is somehow the game's global save file has become corrupted. In this case, the best thing to do is go to the folder you've saved the game in, cut and paste your numbered saves and 'persistent' save file elsewhere so they're backed up, then delete the current version of the game and redownload it again from this website.
You should then be able to copy your backed up saves into the new game's files and continue as you were...!