Well, (if you're talking about gym badges) say if you add all badges to a save that has only one badge of course it wouldn't accept it. You should try just copy/ pasting Pokemon and known items to a new save.It didn't go well because i used the oldest save i had and i had to put also the badges and all and when i started the game it was glitched as hell, i didn't have the Pokémon, Pokédex section in the X menu and i didn't have the C-Gear, and the badges menu wasn't really good, the badges were glitched