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Once you get a book into Calibre then it is up to you whether you keep the original as well. It seems to depend on personal preference. I let Calibre be my master database, while others like to keep copies outside Calibre.
Having lots of books can slow Calibre down slightly - but here we are talking about numbers like 10,000+ so if you are new to this it you are unlikely to get there very quickly. Having said that I have seen others talking about handling 50K books without too serious a perfomance degredation. I personally have over 15K books in my library without performance issues.
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