Hello! Which game are you trying to edit? It's completely normal for the ROM to shrink, don't worry, it's because the tool trims it. However, it's the first time someone has told me Pokémon battles have stopped working. Make sure the unmodified ROM is not corrupt. Also, are you trying to edit battle texts? The game expects some variables to appear in those texts, so if you're editing them that may be the reason too. Regards :)