anyway to change the flag texture in CTF maps without affecting the original files?

You should never alter the original gamefiles..

so

find the skin you want to change
extract it
alter it
place it in a NEW .iwd file in the correct folderstructure.

Tada.

lol caretaker ..totally agree with leaving the original files cuz the game will be reference to a "bad" .iwd and wont run..

and i was actually trying to find the skins u r talking about but there r like three flags ( one for the map , second on the screen , and the third which is the real one in the map) and i couldn't find them?? which also makes me ask if they r all
DX1 non-alphas or should i alter them each in a different way?

thanks

"flag_american", "flag_german", etc. The other images you're talking about would be named "compass_flag_american", "objpoint_flag_american", "hud_mpflag_american", etc.