The Problem is, Calibre imports the books. It is not like Media Player or other Music_Programs. So it never does anything to the original files. As I said, the most simple solution would be to just use the calibre library from now on and delete your old library. Handle all things e-Book through calibre and you are fine. Depending on what you do with your e-Books, this has some advantages. To find and manage books is much more easy in calibre, than in a folder structure. You can send books from calibre to reading devices. How they are named on that devices can be customized with templates even on a per device case. You could also have calibre act as a server to have remote or wireless access.
The other solution is what itimpi has said. Make a template and save the books in a structure you like. In both cases you do not need your old library any more.
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