Only a single font family (Atkinson Hyperlegible) remains active when I restart Fontbase. Windows 10 22H2, Fontbase 2.21.0.
Hello Will, thank you for your post and welcome to the forum 
The topic title and actual post seem to say different things. Could you please clarify what exactly is the issue so that we can help resolve it as quickly as possible?
Thank you again,
Sorry for the confusion - Fontbase was “forgetting” my favorites. I don’t remember the specific circumstances that lead up to this, but it’s possible Fontbase didn’t shut down properly on exit? It seems to be properly saving my favorites between quit & loads now, though. I’ll update this if it happens again and I have more details.
Thank you for the quick reply
Indeed, it’s possible you had automatic collection sync enabled. It saves collections when closing the app. However, if the computer is e.g. shut down without existing the app, there is no time left to properly close and save everything, so next time FontBase is launched is looks for the auto-sync file, which has older data at that point, and imports it, rewriting the collections. Could be the case here. Although it would happen to all collections, not just Favourites 
Thank you again,