Ah youre talking about battle chars, well the textures are stored inside ??ac ??ad, so all you need to do is to put your texture there. Anyway you can just use ??ac and leave ??ad but if you wanna put the weapons textures all together, use that file too ^^.
Stupid question indeed, you have modded battle.lgp and char.lgp? no because modding only one of them will make you change only one of them XD, or probably you changed the final battle cloud instead of the normal one. If you dont wanna swap the files inside battle.lgp just swap the cloud type from ff7.exe
