Well while doing a Root Canal, the nerve from all the canals should be extirpated. Leaving one canal unprepared means that the infection is still there and it can further lead to root canal failure. 

Most probably your one canal might have encountered with ledge. So,  its necessary to break it. Either you talk to the dentist who is doing your treatment or you can visit a specialized endodontist but dont put crown over the unprepared or partially treated tooth. For more info visit the link..........http://www.identalhub.com/articlecategory-root-canal-therapy-17.aspx