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I don't use or recommend using Reader for PC if you want ANY semblance of control of your books on the device itself. Sync syncs everything. Period. End of story. Once items are synced you can't remove them from the device unless you resync then select selective sync but then it removes all the books from your reader and readds everything that you've chosen to sync.
It's a PITA. I don't use Calibre *yet* to manage my books. I just drag & drop them from my computer to my reader.
If you want to stop using Reader for PC to manage your books on your device then make sure you turn off the setting that automatically starts Reader for PC when your device is connected to your computer.
Good luck! I love the reader I just really hate the software. I wish it didn't change from the previous version but oh well. Nothing I can do about that.
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