Tip: You can use Lunar Magic's Overworld Layer 3 Editing system to edit or create your own layer 3 images (castle bricks, fish, rocks) and apply unique effects per level via the Layer 3 Bypass in the main editor.
Not really, but you can use this method:
1.) Open the edited OW in Lunar Magic
2.) Export all palettes of the OW (there is a button in the Paletteeditor)
3.) Then open the new ROM
4.) Go to the OW-Editor and edit a random 8x8 Layer 2 tile.
5.) Import all palettes back.
6.) Click on save.
This should import everything into the new rom, even Events and some small stuff.
This method is a bit older but works. There it mentions to redo the palette, the new LM can import/export palettes.