I have also been affected by this annoyance, from time to time. I wonder if part of it has to do with badly formatted epub files, I have been slowly going through all mine and have found rather shockingly that many have some sort of defect (at least Sigil's check tool says so). I have also reduced the number of books on my device to a minimum, which at least makes the reader respond a bit faster.
I am considering to just reset it (again) and only load one free kepub from Kobo's library and one properly formatted epub just to see if it freeze.
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