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Since I load an SD card on my computer instead of loading directly to my device, I have a custom column that I made in calibre that tells me if the book is in my reader or not. I delete books in the reader as I read them so when I go to reload the card, I just check the on reader column with what's left on the card. If it's not on the card, I remove the indicator from the on device column. I also update the unread column.
I also put no more than a couple dozen books on my reader at a time. It makes managing them easier, the reboots needed when I change batteries are shorter, and a couple dozen books on my reader will last me for weeks, if not months, since I don't read it at home (I use my computer, usually in conjunction with my 32" TV screen)
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