Dont save the texture in pk3, just replace it

the problem being that once the texture of the flag is modified by layer by copying and pasting on top of another flag, with GIMP, I can no longer switch from the pk3 format, and it remains in .zip or .tga, I don't know how to put it back in pk3
ehh... are we talking about the server? or the client?

Client:
Cannot swap textures because the server is using different ones. VPN only

Server:
If you want to do this on your server, then texture swapping will work.