Patricia -- how many books do you keep on your Kindle? I've noticed a slow down if I keep all my books on it, so I've cut back substatially. (I think I've only got about 200 on their right now.) All the rest are in Calibre, and I'm using Calibre to manage and edit Collections (with the Collections plugin).
One thing about using Calibre for this, is that you don't much care if you lose what's on the Kindle, since it's trivial to re-create from the Calibre database.
Also, getting low on battery (which it sounds like happened) can be an issue. (And IME, the Kindle isn't all that good about showing current battery level. ) But I suspect that abookreader might be right about indexing being the issue.
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