Hi ultimaweapon, maybe I can help since this seems doable through the editor
I relocated palace 6 and the Great Palace to where palace 6 was and hidden it.
This is what I understood from that:
1. You moved the area warp of palace 6
2. You moved the area warp of the great palace to where palace 6 used to be
3. You set the Y coordinate of the great palace's area warp to 0
If that's what you did, then here's what's wrong:
As trax said, the game just "draws" a palace tile when you play the flue and it moves the area warp of palace 6, NOT the great palace. So you probably saw the drawn image of a palace but it's just that: an image tile.
Here's what I suggest:
1. Undo everything you did with the moves and such.
2. In the editor, in area editing mode, click any area to select it, then right-click it. (Yeah, it's a bug that you gotta left click first)
3. From the drop down menu, click "Seek Index..."
4. Type 53 (that's the index of palace 6's area warp), then click OK. (in hex it's 35 like trax said, but 53 in decimal)
5. You'll see the view go all the way up north since palace 6 has a Y value of 0. You can't click it since it's out of bounds, but you can change its properties.
Change the scene and world to the appropriate values that you want. (Probably scene 0 in Great Palace)
It will work. (I've done this before.) BUT you will need to fix the graphics of the great palace when you enter. Maybe trax can help you with that...?
I hope this information is what you're looking for!