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I long ago took to running Calibre itself on only one computer. All the files on that computer appear on several others (because they are in a Dropbox folder) but I also don't make any changes to the Calibre folder on any other computer.
I access Calibre on the other computers using the server--which works well for finding books and downloading books. I add files to Calibre from other computers by adding them to a folder ("Add2Calibre") in my dropbox folder but not inside the Calibre folder. I set Calibre to automatically add files in that folder. (Add a file to that folder on another computer results in the file appearing in the folder on the Calibre computer and then Calibre noticing the added file.)
This is the strategy I use. Maybe it will work for you.
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