I have no idea what you mean. But it sounds to me like a dupe issue when you use transfer and refresh or something like that. When transfering a dir several times IoNiNJA will unpack and delete the dirs but you script do not recognize the dirs as complete and therefore upload them again.
Since ioNiNJA is not a dupechecking script there is no real way for it to block recreation of CDx dirs etc in root directory. You must check nXTOOLS or your transfer script for a way to dupecheck either the files or CDx dirs.
As for the other error I have no idea.
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ioNiNJA
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