I just re-read the Qu-drive instructions/recommendations and two things stand out:
It is recommended to off-load projects rather than continue to use the drive with multiple projects stored on it as file fragmentation can occur and affect the write speed. This is one likely explanation for skips starting to occur where the drive had worked previously. The problem occurring after the update is likely coincidental to the actual cause.
Re-formatting the drive between projects is a good idea. Of course, off-loading the files to another drive or computer is implicit in this.
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