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What I do is have a script (monit on linux) that watches the timestamp of the calibre database file in the sync'ed folder (dropbox for me). If the timestamp changes then monit runs a script to restart calibre.
My calibre restart script kills calibre, copies the database file to /tmp, sets the environment variable CALIBRE_OVERRIDE_DATABASE_PATH to that new copy, then starts calibre. Total calibre-off time is seconds.
This technique ensures that the database file in the sync folder is open only for as long as it takes to make a copy, reducing sync failures to almost zero. A failure can still happen, but it would require two syncs within the monitoring window of the script.
I don't know what you would use to watch timestamps on a windows system.
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