I didn't have that many (at least I don't believe I did) but the update TomTom did to the device when it was pulling the new GPS fix data cleared out all the favorites and recent destinations. It apparently does a restore factory defaults as part of the update. POI's are not lost.
Once the device was updated, you could no longer control it from the desktop, five or six upgrades later (really, you would do it, restart it, do it again, etc) the desktop control was restored.
Apparently it's a fairly common problem with this update, there's a page here
http://www.pocketgpsworld.com/module...517&highlight=
on how to restore your favorites from a backup file to a POI set, not again as favorites.
Word of advice - before you allow this update to happen, make a backup first if you need the favorites and the rest. I don't have enough to go through that, but know some people may have considerably more.
This has been an issue for several weeks apparently, there are websites mentioning it back to October.