Lmao... it could be a part of the game. However, if the issue is blocking you from playing, tell me so I can look into it. If the game was uninstalled on its own, it could be the anti-virus going nuts ^^
I think it was just a glitch! I reinstalled it with the itch client and all of my saves were still there. Working my way through a second playthrough now after getting ending 10 I believe. Very nice game, it's fantastic so far.