Some final code requests (and screenshots)

Ok, so I just stumbled across a pretty sizable bug that is also present in the General Leo Edition. In vanilla FF3, when you complete the floating continent and "wait for Shadow", a flag is set that makes Shadow appear in the Veldt Cave. When this flag is set, it also allows you to immediately go to Owzer's Mansion in the WoR (after getting the Falcon) and find Relm there. If the player does NOT wait for shadow in the floating continent, Relm will appear in the Veldt Cave instead, and the player will not be allowed to visit the dungeon in Owzer's Mansion until Relm is rescued from the Veldt cave.

Now, I am only theorizing that this bug originates with a change that fedorajoe made so you don't have to "Wait for shadow" any more on the Floating Continent. The characters immediately jump to the Airship. This seems to incorrectly set a flag so that the player can immediately go to Owzer's Mansion to recruit Relm, OR go to the Veldt Cave and find Relm wounded. Basically, you can do this out of order now. This causes all sorts of problems, like massive plot holes and seeing two instances of Relm if you recruit her in Owzer's Mansion first.

Does anyone know how these flags work, and how to fix this bug? I also don't want any fixes to interfere with the fact that Leo can be obtained immediately at the Colosseum by betting the correct item.