Absolutely. You may need to see what rights you give away when the short is published (many outlets nowadays only ask for the first rights and you can do what you want after six months at the most), but there's not likely to be anything to hang you up.
The rights are what concerned me. I thought publishers wouldn't want the novel if part of it was tied up elsewhere. I know I'm thinking too far ahead considering the story isn't even finished, but, that's what I do.