Let me guess.
You download the zip, and extract it on top of the old installation, yes?
Don’t. It leads to issues like this one.
If you don’t want to use the itch.io launcher, just download the zip, extract it somewhere and then run the game to make sure the new version is picking up the saves you had.
After that, feel free to delete the old version.
But never overwrite, sometimes it’s safe but you never know when something might go wrong.