Just delete the book from the "eBooks" folder on the internal drive that appears in Windows Explorer (or whatever) when you connect the Gen3 to your PC. Two drives will appear - one for the Gen3's internal memory; the other for the SD card. The internal one is the one with the "System" folder on it.
I don't believe that you can choose auto-sync or not on a "per-card" basis. It can only be turned on or off for the device as a whole. Personally I prefer to copy books manually to my Gen3.
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