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This is not new it has been the way Calibre works for at least 18 months. Have you been using both Calibre and Sony's reader software to send books to your device?
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Yes I have, for stuff like books from Project Gutenberg I'd use the Sony software and add all of them to one collection because it was faster than importing into calibre since they were already in epub format.
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What were you doing when you noticed extra collections?
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Well I had just update calibre, so calibre is what I was doing!
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I have unchecked download tags in my metadata download plugins (under preferences - Plugins) in each Google, isbnDB, and Amazon. This stops tags from automatically being added when you download metadata.
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I just did that, thanks for the tip.
Is there any way I can edit the metadata of books on the reader which are not in the calibre library? (800 books and 450 collections, haha)