The Itch Launcher has a glitch where it will occasionally erase manual saves (autosaves will survive, but they've been broken for the last two updates sadly). As it's on Itch's end there's nothing I can do about it, unfortunately.
If your autosaves are missing then the only thing I can suggest is to visit the CK Discord server and grab a save file from there. There's a start of Act Three save pinned in #game-chat, and people in #game-help are happy to share saves if you are looking for one from a different point in the story.
Sorry for the inconvenience!