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Originally Posted by durtreg
However, the first time the books were sent to the device (on linux-calibre), the properties were not on the device (I will look into this when I get home to my linux machine). They should have been handled the same way as here at my work computer - the right way. I will check if this is the result of some difference in settings between the two calibre installations or indeed a bug in the Linux implementation of the pdf writer.
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You're right, sending the books to device via Calibre ought to have updated the metadata even on Linux. I can't help you with that, though, seeing as I don't run Linux. Checking the config may be a good idea, though.
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I am now convinced that the behaviour I see is a result of the above mentioned Sony-XML-Metadata getting out of sync with calibre. It would explain other things like disappearing books on the device.
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Several things come to mind here: If you have automatic metadata management turned on, Calibre will change the collections if you edit certain metadata fields. This might make books disappear from one collection, thus seemingly getting lost. Another thing is that, if you have two independent Calibre libraries set up on your home computer and your work computer (by independent I mean not synced by, say, Dropbox or something similar) then the internal book IDs may differ in between the libraries. I don't know how Calibre determines which book is which, but I have a feeling that the ID might be involved. Thus, the two installations would probably get confused about which book is which.