Calibre handles this very well. Plug in kindle > open calibre > go to device settings and uncheck pdf support > add books and calibre automatically converts to .mobi
Maybe I misread the link I shared. Can you clarify:
> PDFs can be converted to the Kindle format so you can take advantage of functionality such as variable font size, annotations, and Whispersync. To have a document converted to Kindle format (.azw), the subject line should be "convert" when e-mailing a personal document to your Send-to-Kindle address.