For anyone who would like to run a test. Take some ePub and run them through Kindleggen and put them on your Kindle. Do not use calibre at all.
Then run other ePub through calibre and put them on your Kindle. Turn on WiFi and let Amazon delete your eBooks and see if the Kindlegen created eBooks still remain.
Thanks.
P.S. Here is a link to Kindleen. It will be good for 7-days from now.
https://we.tl/t-Vf2kMUqNGI This is a command-line based program for Windows.