I came a bit late to the Calibre party, and had to add a lot of books. As Harry says, do it in pieces, making sure your metadata is just how you like it. Make sure to back up your calibre library. And use Calibre Companion on your reader. I have all 10k+ books on my reader, and am able to sort by tag, date read, date added to Calibre, etc. I am very happy (not as happy as I will be when the Cubs win the World Series, but pretty happy).
Debra
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