Map graphics error and wrong location name

On a side note, I once had trouble when using the warp spell to escape from my custom dungeon, I landed on a completely different place of the world map, unable to reach my airship again. This issue was solved when I set the unknown bit 3.1 for my exit. I did a bit of testing by clearing bit 3.1 from a few world map exits, and found that without this bit, returning to the world map became messed up. So I guess that this unknown bit 3.1. seems to be needed for having the warp spell work correctly (perhaps the spell 'remembers' the last exit that had bit 3.1 set, and warps you there?). Can you confirm this?

I have no idea what bit 3.1 does, could it be the "Refresh parent map" bit here?

Maybe, if the 'parent map' is the one remembered for the Warp spell. I'm not really sure, I just got that idea because I saw that bit 3.1 is set for all world map exits (except the one for Baren Falls, but since you can't use warp in that area anyway it wouldn't matter), and is never set by any other exits.