It happened several to me several times that I updated my TomTom using TomTom HOME (software version, maps, etc.) and after that all my favorites were gone.
To restore them, just find the backup folder on your computer, which is for me
or in earlier versions was
In there you should find a directory like
which depends on the map you have.
In this folder is a file namen MapSettings.cfg. Copy this file to the TomTom and your favorites are back again.