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there's no way to skip it, i'm afraid. there are chunks at the end of those wave (aif) files that may not even be present (or current firmware version). I expect it does some alignment so that they're always at specific places, and are large enough, etc.
hey @ludicrouSpeed I just transferred some old saved tapes for a remix and got the defrag too! This is the first time I've actually transferred tapes from backup - is it the default operation? Doesn't bother me too much