There's an overwrite followed by a hard reset going on with updates which kills off your favorites, recent destinations, etc.
Use "Add Community Content" (see the MyTomTom systray icon) and you will find that you can copy your "Favorites" to your PC, and then reload them again later. They'll be saved as "favorites.ov2" on your PC. Oddly, custom POI are not bothered by these updates, but Favorites are.
I always keep a recent copy of my favorites.ov2 file before doing any firmware or map updates.