Im not sure if I fully understand what you are asking, but would zipping up the entire thing into a file that doesnt store filepaths then unzipping it wherever you want accomplish what you want?
Ive done this with roms as I was messing with the GoodTools directory options. I use the Store option for compression to make it faster.

Then make sure you dont have it store paths, so when you extract it, all files will be in the same directory.

Once you have all your files in the same directory its easy to zip up ones that arent zipped already.
My apologies if I misunderstood the question completely, I am on my first cup of coffee after all
