I extracted it using 7zip. Oddly enough, the values are normal now after I checked again to be sure that it was a .gba file. It was one! Now, when I edit the values and go to play it on VBA, the values do not change in game.
So I change the values, load the modules to the rom, then save. Then, I close Nightmare and open up VBA and Sacred Stones, but the stats are the same.
Thanks for the reply and answer, by the way! :)