That's very strange, I'd like to think it's a quirk of the itch updater.
Is this on Android? I've had some problems with Android saves in the past but I can't see how it'd happen to a windows save. If you have to access the save files for any reason on windows, they're in %appdata% -> roaming -> moncurse.
I'm going to keep trying to see if there's a way this could've happened but do check you're on the right save (1/2/3), just in case!