[7hir7een]

For what it's worth, here's what I did exactly. In Calibre v0.9.4 or above:

1. Deleted old converted files from the Kindle first. I had used a variation of Gazella20's method before (way too much work)
2. Highlighted the files in Calibre I wanted to convert and hit "Convert books"
3. Selected MOBI from the output format dropdown menu
4. Used the settings shown in the attached picture
5. Hit "OK" to convert to MOBI (again)
6. Waited for that to finish
7. Connected Kindle Paperwhite
8. Highlighted all the converted books and hit "Send to device"
9. Waited for that to finish, ejected, waited for the books to show up on the Kindle, and made sure everything was good

This should really work, so you may want a try a couple this way and see what you get. You shouldn't have to go through all the work of the old way with the metadata editor.