If you're fine with using cheats, you could try to:
- Enable NoClip in your game when you manage to go back to the merged world. This allows you to walk through the sea and go back to Branch Castle and retrieve your airship.
- Take a save in the merged world and edit the save so your coordinates are at where your airship's coordinates are.
- Have a save in Branch Castle, edit the map file for Branch castle to have a transfer point to merged world only. Branch's Map is located in www/data/, Map317.json.