Did you only use autosaving as your main and only save slot? There is no reason why this would happen. A crash during an autosave could indeed corrupt the save file but not multiple different ones. Does your Game gallery on the main menu show stuff unlocked still?
I really wish I could figure this one out. As a last case remedy, check if the game you are opening the same one, maybe you have more than one version on Itchio, and you opened a different one after the crash. If not, check if itchio downloaded an update while you played which caused the crash and overwrote the saves. Other than that, I can't really think on what could cause this. I am very sorry.