Sorry - I assumed since this is the conversion forum, and your profile says your preferred reader is a kindle, that you were converting from epub to kindle format.
Are you converting *to* epub? It looks like the same settings are available there. You can also embed your preferred font during conversion, which will probably work, depending on your reader. I used to embed my preferred font in my books, before the kindle allowed user-installed custom fonts.
I handle this kind of thing in the calibre editor - I remove all font-family settings from the CSS classes used for "open text", so the font settings in my reader (usually kindle PW4) are used for all books.
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