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After a lot of fiddling about it looks like it was database corruption, though I’m not sure what caused it. I’ve now successfully removed all trace of the book and added it again using Calibre and all is well. For a while there I could delete the book but a database ghost entry kept coming back.
Hopefully the other odd behaviour—incredibly (sometimes infinitely) slow reaction to unplugging/plugging in—will also disappear now.
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