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Firstly, I'll admit to rarely using "Copy annotations for Selected Book". It seemed to work the last time I tried, but it wouldn't surprise me to much if it is broken a bit.
To start with, can you run calibre in debug mode, connect the Glo and copy the annotations for the book that is having trouble? Then either post or PM me the log file.
If that doesn't help enough, a copy of the database from your Aura and the annotations that did get copied probably will. That way I can try and work out what is common about what is being extracted and what is not. Either put the files somewhere I can download them and PM me the link, or PM me for an email address to send the files to.
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