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Someone will be along eventually who really knows what they are talking about, but here is what I understand. Calibre is not designed to be networked. Work is proceeding along those lines, but is not there yet. There are definite issues with accessing the database with different operating systems which do or do not consider capitals in file names significant. Fiddling around with the calibre database and its files outside of calibre is all but guaranteed to cause corruption because the program was not designed to create a standalone database. You might be able to organize files with calibre and export the results and use the results saved separately any way you wish.
Wish I could help you with the rest, but that is as far as my understanding runs.
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