Sounds like to me you're editing the size of a movieclip, inside of movieclip, used for another movieclip to. For example:
Movieclip A > Movieclip B
Movieclip C > Movieclip B
Both movieclip A and C have movieclip B in them, so editing movieclip B will edit the way movieclip A and C represent movieclip B according, based on the way movieclip A and C are scaled.
Did I lose you?
Anyways, what you need to do is make it so movieclip C has a version of movieclip B, different than that of movieclip A's movieclip B. Just go to the movieclip B in movieclip C and right click it, then click "Duplicate Movieclip" now the movieclip B in movieclip C will become it's own movieclip, movieclip D making:
Movieclip A > Movieclip B
Movieclip C > Movieclip D
So feel free to edit movieclip B and movieclip D however you want and it will not !@#$ up the size of the gun represented in movieclip A and movieclip C.