I have a very similar problem with my PRS900 - but in my case it's not the number of books, it's the number of annotations on PDFs that is slowing it to a crawl - both in terms of building the database when booting and both in terms of saving notes/annotations.
With 100 PDFs each with 10-20 handwritten annotations, adding one more annotation then turning page will take about 2 minutes.
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