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When you import books into Calibre it creates its own database of books using its own naming conventions. The original books will still be there untouched.
I found in my case all problems were avoided if I put the Calibre library folder at a location other than the existing root of my existing eBook library to avoid just this issue.
Sorting it out should be relatively easy - it is just a case of moving the new folders/files created by calibre to a new location and then telling calibre to use this location as its library location.
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