Okay I think I see why this is happening now. This is an issue that occurs when you run the game with the "itch sandbox" mode enabled.
I'd recommend copying your save file from the itch profile to your main profile and running the game executable manually/with the sandbox feature disabled in the itch launcher.
Your itch save data will be stored in a folder that looks like this, with a slightly different itch id. Be sure to turn on hidden folders if you're have trouble finding the full path.
C:\Users\itch-player-5f1e0bcd\AppData\Roaming\Oneshot
Then copy everything from this folder to your main profile, that is, a folder that looks like this
C:\Users\<MAIN USER NAME HERE>\AppData\Roaming\Oneshot
It's possible the Oneshot folder won't exist in "C:\Users\<MAIN USER NAME HERE>\AppData\Roaming" yet, so create it if it doesn't.
If you do this, you should be able to launch the game executable manually and still have your save data, and then run the clover.exe as well to continue the game.