The same thing happened to me. The only thing you can do is to browse into your TOMTOM disk, search for the file mapsettings.cfg, save it to your local machine and do the map update. After the update, copy this file from your local machine back to the same folder. Then you preserve all your favorites.
Instead of marking a point as favourite place, why dont you make a poi category called "favourites" and keep adding your places to favourites category. That way, you can even add a phone number to the location.
You can make a backup of it in .ov2 or whichever format you like.
TomTom's mapsettings.cfg is incompatable between navcore versions.
I also figured out that the mapsettings.cfg file causes rebooting loop problem. It can be fixed without loosing (deleting) your favorites:
1. Connect your Tomtom to Home and hit the "Operate my..."
2. Add a random address or location to your favorites
TomTom will rewrite the file mapseeting.cfg to the right format and you get rid of the rebooting loop without loosing your favorites.
Tomtom GO 730
Map: Australia 8.30.2352