Sounds like BC is trying to outsmart you. I think it prefers to maintain copies of the same route, track, waypoints in different folders, but they are all the same.
I split and combine tracks a lot in Mapsource. I first copy the track to the clipboard. Then I edit, rename, and OK the track. Then I paste the original from the clipboard back into my work area.
I think I have also done this in BaseCamp. As long as you have a copy/paste feature, it should work.