title_body: What happens if I have used 2 different fonts in mobi/epub and user changes the font in the devise?
upvoted_answer: There isn't much you can do, if the device allows to change the fonts and the user is willing to use that option, he will do it.
  
  If you use different fonts not just for aestethics, but with a functional purpose (i.e. to display code with a fixed width font, or to differentiate quotes from default paragraphs, and so on), your best option, IMHO, is to insert a disclaimer where you explain this to the end user.