I use Calibre as my ebooks management software transferring titles via USB to my Kindle Wi-Fi unit.
According to Amazon Kindle support service, this strips away the codes allowing for synchronization between my Kindle and their "Kindle for PC" software as well as preventing any backing up or transfert of the annotations & highlights which I have so far jotted down on my Kindle Wi-Fi unit.
This means I will lose all of those if anything happens to any title on my Kindle Wi-Fi unit.
Any suggestions about avoiding this ?