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The key to using Dropbox with Calibre is to realize that, so long as Calibre and the Dropbox daemon are never running at the same time, the risk of corruption is no greater than with one or the other alone. That said, be aware that Calibre is still running even when the main window is closed if there is a viewer window open. I could not find an option in Calibre to close the viewer windows automatically whenever the main window is closed. So to use Dropbox you need to be sure to close all Calibre viewer windows and the main window before running the Dropbox daemon. I have scripted this condition in linux as well, for myself. The code will be very system dependent, so not including it here.
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