Level Editing

This may be one of those "Really? You're really going to ask this?" questions but it's pertaining to the level editor. I am aware of the whole "Use a fresh rom to edit blah blah blah" stuff, so we're past that, now here is what I am thinking.

1. I edited a roms overworlds to replace chocobo stables with a warp facility outside most major town locations.

2. I used save point npcs as the graphics for where the warp points were in the "stables" and linked all warp points perfectly.

3. Upon testing, the WoB and WoR stables graphics were laid on top of eachother and the save crystals appeared as still glitched fire.

4. Now that the map is no longer editable in this rom, is there anyway to remedy this without having to start all over again? lol Thanks for reading!