You could suggest the main site that should be considered to the same category and include a note in [ ] stating that it replaces the previous url which was already suggested and why. That should be sufficient to over write the existing suggestion if it hasn't allready been changed by a reviewing editor. If the site is clearly a sub-site of another, a reviewing editor will in most cases change the url manually upon review and either review the main url then or leave in unreviewed for later depending on time and other current projects.
Hope that helps.