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No, I wasn't running both simultaneously (I may be crazy, but I'm not stupid). I used Calibre to import some .txt files (and reformat to ePub), and write them to the reader. Then I opened the reader software to assign them to collections (this had worked well before). I had previously set up the collections in the sony software, and the Calibre tags seemed to have no effect, at least at that time. Note that the new files had no tags at all. I opened the sony software to assign the new files to collections, and discovered all the new collections, with all my previous books assigned to new and different collections. I just spent most of the evening deleting the new collections and reassigning books to my preferred collections, and would really prefer to NOT have to do this again. Can I tell Calibre and/or Sony to ignore any tags, and NOT create new collections on the reader?
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