That's a pretty blatant oversight indeed!
Simply put, those 'flags' are 'event bits' and are used for setting and clearing various event-related things, to control what happens or appears at certain points in the game, or what have you.
Assuming you'd want Relm to be there in the cave, a fix could involve using a different/custom/unused event bit instead that would basically do what the 'left Shadow behind' bit did in terms of putting Relm into the cave, but it would have nothing to do with Shadow at all so it wouldn't effect him or any code that was left behind that could effect Leo, and then in-turn update the Owzer mansion and Veldt cave entrance event and/or memory bit stuff to the new bit.
I think that'd be about it anyways.
Simply put, those 'flags' are 'event bits' and are used for setting and clearing various event-related things, to control what happens or appears at certain points in the game, or what have you.
Assuming you'd want Relm to be there in the cave, a fix could involve using a different/custom/unused event bit instead that would basically do what the 'left Shadow behind' bit did in terms of putting Relm into the cave, but it would have nothing to do with Shadow at all so it wouldn't effect him or any code that was left behind that could effect Leo, and then in-turn update the Owzer mansion and Veldt cave entrance event and/or memory bit stuff to the new bit.
I think that'd be about it anyways.
We are born, live, die and then do the same thing over again.
