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I have never had that problem. Sorry I can't help. The only thing I have to offer is don't unplug it during a job and then plug back it because it won't work. You have it plug it in before you start a job. But that wouldn't cause intermittent problems.
Ida, it sounds like your USB drives are going "to sleep." That's a setting.
I had a similar problem many years ago on Eclipse where the audio would just cut out for several pages and then start up again. Turned out the sound quality settings were too high on my codec. I think I had it on like stereo studio quality or something like that. It was creating such huge sound files that the computer just intermittently stopped recording, I guess to catch its breath or something. Might want to check your settings.
I don't know what software you are on, but in Case, if you're playing back audio and you have it set to "skip quiet audio" it will jump around. That happened to me, and I thought something was wrong with my audio recording. Once I put it on "no skip," it worked just fine. Good luck.