I use Dropbox, not Box.com, but the theory is the same.
Before starting calibre, I start Dropbox and make sure it is fully synced.
Pause Dropbox.
Start calibre.
[...]
Close calibre.
Resume Dropbox, make sure it fully syncs.
In other words, make sure that everything agrees at all times, and don't let them run simultaneously.
There is no especial trick except being diligent about not slipping up and running calibre without making sure that Dropbox is synced first.
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