I would have looked into what produced the problems in the first place. One safe thing to do, is to create a new cloop device, loop-mount a (copy of a) KNOPPIX image on that, and rsync it into a directory for further remastering. That should be unproblematic, no open files, no special files etc. I also wonder why you care remastering Knoppix 6.2,X, as quite a few bugs from these versions are fixed in 6.4.4, and you might get version conflicts working with older packages.