I've been investigating a fix to the "level reset glitch" in the Advance version of the game. By my understanding, there's a variable in both the SNES and GBA versions that tracks which save file was most recently loaded or saved. However, in the SNES version, the only way to return to the title screen is by using the Reset button; in the GBA version, there's a new Quicksave feature that lets you save (in a special slot) and quit your game and return to the title screen. You can then resume your game using the Continue option.
There's a glitch here that players on the GBA version can exploit. If you save your game in one of the three slots and then Quicksave, then start a new game and get annihilated without ever saving, the game will reload the previously saved game, but your characters (that you found in the new game) will have the same amount of Exp. that they had when you died. This essentially means that you can revert your level 99 characters in Dragons' Den to level 10 or so.
What's interesting is that when you start a new game, the Quicksave data gets erased. My guess is that somehow the "recent save" variable doesn't get cleared properly; however, my efforts to find the cause of the problem in the code have been fruitless. If anyone knows where to find the Quicksave and/or New Game functions, please let me know!
On a side note, I also discovered that the Chain of Command Bug (which I have fixed for SNES) also exists in the GBA version, but I cannot find the relevant code for that either. For that matter, I can't make sense of any of the menu code in the GBA ROM and trying to comparing it to the SNES version is not of much help.