As theducks said using send to device should only send one format.
To be doubly sure:
go to preferences>plugins>device interface plugins and click on your particular kindle plug in.
Click customize and make sure epub is unchecked. It should be by default, but sometimes one changes things.
Another reason to keep the epub is mobi files have nonstandard (depending in how you define standard) metadata so if you use book jackets for example and reconvert you get an extra jacket and extra page.