When you save a map as "Final" protected, close the map immediately after saving. To continue working, just open your non-protected copy again. If you try to save as SE-Compatible after saving as Final, the map will still be protected. Therefore if you later save over your non-protected version because you thought it wasn't protected, you will lose it even if you select "SE Compatible."
If you have done this, running the map through SCU under "GUEdit" unprotection will reset the location names back to the default (Location 1, 2, etc) and you should be able to open the map again.