As someone already pointed out, deleting collection ON the device is pretty easy. The only issue is Calbre re-uploads them by default next time you plug in.
I like the auto tagging in Calibre because it auto updates all meta-data when the device is connected. So I can use Calibre to suddenly make 5 books part of a series and then I don't have to reload them as new books.
I was annoyed when Calibre first added the feature (it wasn't there when the 650 first came out) but once I understood how the auto update worked it was easy to make the tags/series work like I wanted.
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