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eschwartz - perhaps you never had to use a 256Kbs satellite link. Not only slow but usually unreliable, particularly when its raining and even worse when there's a storm. And expensive to boot, and that's a recurrent expense, not capex. Every kilobit matters in that scenario no matter how you synch.
to your suggestion to use a file synch product to filter out the unwanted file types. But, that's a cure...
When a format that's already in the library is sent to a device calibre updates the metadata in the file that's sent to the device, but it does not update the metadata in the library copy.
So when a format is created specifically as part of sending a book to a device why should it be saved, surely that's inconsistent? Not saying the possibility to save shouldn't be there, or that it shouldn't be the default, just saying that to be consistent there should be an option to not save it.
BR