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Calibre is not meant for using on more than one device. Library corruption will result, as you've discovered.
Yes, the only option is to add the extra titles manually. That's because this is not supposed to be a regular occurrence, but an one-time mishap. If it happens regularly (as it always does when two-way cloud syncing is involved), then you're doing something you shouldn't (like using two-way cloud syncing).
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