There sure is! Select the books in question, then click the down arrow next to "Remove books." There are a few options to accomplish what you are looking to do. Just pay attention to whether you are selecting a format to KEEP or DISCARD and choose accordingly. Sounds like you could use "Remove all formats from selected books, except..." and select EPUB.
I'm no expert with this great program but I've picked this up- don't make changes to the Calibre library outside the application (such as deleting files from Windows). From what I've seen, Calibre has all the tools to manage your digital library. Making changes to the library outside Calibre is just asking for headaches.
Good luck and please check back in with any questions!