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Personally I would suggest you rethink putting 3,000 items on your device. It will always be your device that is the weakest link in the chain slowing things down - the more books you put on there, the slower it will be every time you connect it to calibre as it has to read the database off it and iterate across its folders to find books that are not in your library etc.
I "limit" myself to around 400 books at a time on my Kindle - still 18 months worth of reading and enough variety to keep me interested, while keeping calibre responsive enough when I plug it in every few weeks to remove read stuff and top it up...
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