the trick is dont replace the gfx just add them and then when its done and rel ported just aadd the same gfxs to the original char i got sonic,knuckles and shadow 2 of them rel ports all working without gfx glitches if they all have the same graphics,reffs,elfs there is no glicthes.
I have an interesting theory:
Remember the effect folder?
You have the ef_char.pac which is separate from all the other characters, just export the ef of the Moveset file to the replaced character on the effect folder, then in psa just change the value to the target character, and there wont be problems and its easier for characters like mewtwo and lucario and kid buu etc, which uses the common gfx for the same attack (NB)
-Like mewtwo gfx be over peach´s effect file in the effect folder.
-Then in psa change the lucario effects ids to peach´s and there wont be problems since peach will be there as mewtwo.
If you didnt understand my strange explanation xD ill test if works then make a tutorial.
I think this is better than getting all your characters have the same gfx. imo