Furst an observation: Disk space is cheap and ebook files are small, so is there a real need to remove redundant formats? You might find at some later date you wished to keep the format.
Having said that, it is easy to remove a particular format. This can be done via the Bulk Edit Metadata dialog. However to avoid removing the only format you currently have, you might want to restrict the books selected using a search term of format:epub (assuming that you do not want to delete epub format books). Having done that you can call up the Edit Metadat option and remove other formats one at a time confident that you have an epub format for thte books in question.