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I delete books I never intend to read again from both my reader and Calibre.
If it's a book I am unlikely to reread, but want to keep for whatever reason, I delete it from my reader and move it to Calibre Vault library.
All of the books in my main Calibre library are on my reader. I love having the ability to choose whichever book strikes my fancy to read at the moment. I haven't noticed any increase loading time to my Sony since I more than doubled the number of books on it in the past year.
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