Yes, the files may seem damaged when copied from a state where there are no protection bits set. I've done this a couple of times: Upacked a zip-archive using unzip, then moved/copied the files using Dopus. Dopus will create empty files in the destiation dir because it is not allowed to read the files. I don't know if there exists a unzip which fixes this problem, but you can make a script that automatically sets protection bits on the upacked files (in eg. Dopus).
[ pegasos ii / g4 | morphos1.4.4 ]