there is a couple of files, the regular texture, the ones where u see through it, etc, i never tried it yet, if u edit a texture, u need to remake a transparent texture also to fit the new one, i used to do it in photo shop way back, i think when u convert it back, make sure its the same format
as the original, dx 5 or dx1 ,not sure, never test it yet, there is only a few format to convert it to, also there is some flag texture outside the flag folder, usually there is a few texture for alpha maps, no idea if this is just one, also alpha is a pain to redo sometimes , i had a prob with editing skyrim once a while

Thanks,I'll try

usually takes time with alpha, sometimes there a pain to learn, i know i had prob way back