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Same Issue
First off, thanks to all who developed Calibre, while I loved my Christmas Sony T1, I thought the sync software was so limiting.
I grew my Calibre library and knowledge. They synced. The first time the collections came out great. Then I started changing the tags and series to make sense. I also downloaded books via wifi. My collections, those sent via Calibre showed up with 'removing' when I wanted to look a them. The count was correct however.
I got a new SD card formated on the Sony, latest Sony firmware, latest Calibre and same issues. I should note I do use the Sony reader to sync my pictures and music, which are fine.
No solutions here, waiting until someone more tech savvy than I can point me int the right direction.
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