Are you using the Steam Store version or just the free version here on itch? If you are using the Steam version, you have to turn off the steam sync before going into app data. Then it may ask you a question of "are you really sure" when trying to resync the info.
It is sort of the same, but Steam has the extra cloud backup off of your computer. As such, the game data gets pulled from the cloud if you use the appdata delete. You just need to stop the cloud link before using appdata and it works the same.
