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I'm not sure if this is as big a problem as it used to be long ago, but badly formed ebooks could cause similar problems to what you are seeing. There is an automatic process that searches the filesystems for ebooks, and then analyzes them and adds the details to the library database. It was possible for a badly formed ebook to cause the analyzing program to run at 100% for a long time, running out the battery and keeping the rest of the ebooks from being analyzed. The only solution was to remove the bad ebook from the device. So, you could try removing all your ebooks, and then adding them back gradually until you see the device acting up again. You might be able to find any bad ebooks that way if that is what is causing your problems.
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