It happens occationally when the files that store the information of what's enabled get corrupted and/or deleted. That's something that seems to happen occationally when having high memory usage and quitting the game. The file gets saved at that point, but it doesn't save correctly, so it's at 0kb, which makes the operating system delete it.
The Instant Return to Desktop mod seems to help avoid it, as it changes how the game shuts down.
https://steamcommunity.com/sharedfiles/filedetails/?id=2037888659&searchtext=instant+desktop
The Instant Return to Desktop mod seems to help avoid it, as it changes how the game shuts down.
https://steamcommunity.com/sharedfiles/filedetails/?id=2037888659&searchtext=instant+desktop