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Never run Calibre on both computers at the same time. Never sync while Calibre is open.
Those two principles are all-important for running Calibre on multiple computers against the same library.
Basically pause syncing, open Calibre, do whatever you need to do with your library, close Calibre, resume syncing. Then on the other computer sync, pause syncing, open Calibre etc.
Still, it's very easy to cause library corruption by running Calibre on multiple computers, so check your library often.
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