Yeah, if you just add a UV Map or another Unwrap UVW modifier to the stack, bake your textures, then delete/disable the new UV modifiers, your initial UV layout will remain unchanged.
You can just add another uvw projection on top of your stack and bake it out to paint on. Then bake that new map out and erase the parts you dont need when you apply it to a new layer in photoshop over your existing texture. You will just delete that temp modifier afterward. Hope I am understanding you correctly.