I have a little more time now...here's a little more detail.
The file Current.gpx in Nav/Garmin/GPX contains your current favorites, custom routes, and active track files.
If you use BaseCamp, it puts data onto your device via the file Temp.gpx in that folder. Those items will automatically get added to your device's favorites and custom routes upon the next device boot-up.
I believe that any other gpx file in the folder will get automatically loaded as favorites as well. At least gpx files produced by Garmin software. I'm not 100% sure about this, though.
Data (favorites, routes) in any other .gpx files in that folder, or on your memory card in Card/Garmin/GPX, will be available for import under the device's Tools:User Data:Import:[favorites or routes].
If you delete your favorites and custom routes, but those items are in gpx files that are still out there, they can be imported again.
If upon bootup, the device sees a new gpx file out on your memory card, it will tell you it's there and ask you if you want to import. But it only does this once when it thinks there's something new out there. Thereafter, it is still out there and available, but you will have to explicitly import it.
The exception here is stuff in Temp.gpx. Whenever you move items from BaseCamp to your device, BC recreates that file with only the new items you're moving. So any stuff you moved previously from BC, then deleted from favorites, will no longer be there and available for re-importing if you've moved anything from BC since. So don't count on that file as a place to save anything (that's why they call it "temp" I suppose).
I know a lot of folks like to put gpx files out on the memory card so the data can be loaded later. Or use it as a backup. I think RL uses this approach.
Be aware this is all BaseCamp. My time with Garmin is pretty recent, so I just started with BC. I'm sure the MapSource concepts are similar, but the details will no doubt be different.
