I too think that your problem is that it is indexing.
I'm not saying you shouldn't keep all those books on your ereader (it slows some of mine down), but you should have a backup on a flashdrive kept somewhere off your property in case of fire or other calamity. You never know when that is going to happen or in what form. Of course, the biggest hassle is to remove the DRM, but I do that as a matter of course when I buy an ebook. I learned the lesson. Lots of people have lost their ebooks when a publisher shuts down.
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