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Originally Posted by joeblowma
Not sure how, as long as CC is only modifying its own metadata info like it currently does when you mark a book as read? Though I suppose I've not actually tried to do that lately while connected to calibre (tests) OK I coulda swore that entering the missing files list forced me to disconnect before, but it doesn't seem to be sending the read mark unless I disconnect and reconnect anyway from either list - did I stumble on a bug that isn't supposed to happen by chance?
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I mixed two things. The word "mark" is overloaded in CC. There is the notion of marking a book read in book details, and there is the notion of setting a calibre mark on a book when the read information changes (CC Settings / Marking books read / Mark updates in calibre). You are right that a bulk operation to do the first type of mark does not require a protocol change. The second one does.
As for the behavior: what you see is what is expected. CC and calibre exchange the read information when the connection is first made. Further changes on either side are not exchanged until CC disconnects and reconnects, or (I think) if you choose in the calibre device menu "Send updated metadata to the device". The reason I say "I think" is that I am not sure of CC metadata will also be sent back to calibre and I am too lazy to look at the code.
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CC saved my butt when the usb port died on my previous tablet, and I've been using it ever since (which now that I look has been >3 years  ) - because it's a great app as-is. Change nothing and I'd still be happy with the ability to track what I've read and do it all wirelessly - fix up my annoyance at having to mash the dropdown multiple times for each book and you'll have a second helping of my thanks 
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I will probably do something with that dropdown. I will wait a bit to see if anyone has comments on the two choices. I lean toward the second -- two buttons to change the value and a "Cancel" button.