Out of curiosity I have tried umounting the Kindle from the xfce4-mount-plugin panel plug-in without Ejecting the device in Calibre.
The device is umounted, as shown by
$ df but remains shown as mounted in Calibre.
Trying to upload a book gives an error message "error communicating with device".
From what I read on the French SolydX forum, it might be linked to a problem with udisk2...
http://forums.solydxk.com/viewtopic.php?f=7&t=1408&p=13719#p13719