Hi! As it said on the main menu as well as in the description of the game, itch.io used to clear all progress every time I update the game. It was not something I could control. The workaround was to play on https://rugbug.net/redmatch2 or download the game, and the reason I implemented user accounts was to finally fix this issue.
If you were playing on rugbug.net previously, please make an account there to link your progress to your online account.