When you create a Route using Trip planner on device, your "trips" are stored in \.System\Trips\ as xxxxxx.trip
When you transfer a Route from Mapsource or basecamp to device, a gpx file is created in \GPX\ as temp.gpx
When you then start your device, the temp.gpx file is read and the .trip files are created in \.System\Trips\

If your route.gpx file contains one or more routes, rename route.gpx to temp.gpx and copy it in device \GPX\ folder
Inside that folder you now should have:
-Current.gpx [your Favorites]
-Temp.gpx [your routes to be read at turn-on and transformed automatically to xxxxx.trip]
-GarminExpressImport.gpx [your Garmin Express restored backup, which you must now erase because all the data in that file are now in current.gpx]

If you don't erase that file, every time you make a "Clear all user data" or "Clear Nonvol" the current.gpx file is erased but not the GarminExpressImport.gpx
So if you now restart your Nuvi, GarminExpressImport.gpx is going to be transformed to current.gpx
But this is your old backup, not including the recent changes you have done since then.
When you want to Backup your Favorites, just copy current.gpx to your PC, Clear your data on device, rename current.gpx to temp.gpx and copy it to the empty \GPX\ folder.

Friendly Advice:
DO NOT USE GARMIN EXPRESS, it creates more problems than solutions...