Do you mean the tags from B&N that clutter everything up? I would be interested to know if there is an easier way as well.
I actually just did this last night. I went trough and deleted all of my sideloaded books off my nook. They were all still in my calibre so I went and changed my tags so all of my tags started with an * so they will show up first. Then I loaded them via calibre and refreshed. Mine look like this *Fantasy, *UF, *YA, etc... And all of the B&N tags show up at the end of the list. It was the only way I could think of.
If you know how to get rid of the B&N drm, I would imagine you could strip it first and convert it with your own tags. I don't know how to strip the drm though.
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