TRANSFERRING RPG MAKER 2K3 MAPS

If you're replacing an old map completely, not adding a new one:
A.) Take note of the map ID of the map you're replacing.
B.) Delete it.
C.) Paste in the new map. Assuming you didn't have any unused map IDs at lower numbers, it will replace and take the map ID of the map you just deleted.
D.) If you DID have unused IDs, just paste in a couple "filler" maps until you get one that has the correct ID and then get rid of the fillers. (I dunno if there's an easier way, but that's pretty simple)

This might be one exceptional case where directly replacing the LMU file might be easier, just rename the new LMU file appropriately and bang updated map.

Whichever method you choose in the end though, Xenomic, go with the one that you and your mapper feel most comfortable with. Both the LMU and the in-editor methods result in the same thing after all is said and done.