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Well, as long as it's on the SD card, it doesn't really matter. If it hangs after putting a new book on, you take the SD card out, put it in a cardreader, and fix it.
If you don't let Calibre create a too fancy directory structure (like author/series/date/number - series - author - date.epub) and you don't have books with funny long titles, chances are you won't be hitting the limit anyway.
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