Have you done a map upgrade? There is a file MapSettings.cfg in the map folder on the TomTom that stores all the settings. This file gets overwritten if you upgrade the map. I suppose it might get zapped by some other means.
If you have used TomTom Home or Windows Explorer to back-up your device then you could always copy the file back onto the device. You'll need to do this manually though.
By default TomTom Home stores the back-ups in My Documents\TomTom\Home\Backups\Go\Backup01\Internal Memory Then locate the folder with the same name as your map, eg United_Kingdom_and_Republic_of_Ireland.
When you plug the TomTom into the PC via a USB cable it appears in Windows Explorer as a drive usually called TomTom. You'll find the same folder structure as in the back-up folder. Just copy the MapSettings.cfg file over (maybe rename the one on the TomTom first just in case you need to roll back) and that should get your favourites back.
It is also a good idea to make regular back-ups of the TomTom. I have had occasion to restore my devices in the past. the older models kept everything on a plug in SD card. So I used to keep two cards. One for day to day use and one for back-up. And I have had my TomTom screw up the SD card, good job I had a copy!