If i understand your problem correctly, then the easiest way to deal with this would be through an automated renumbering.  Here's Autodesk's version which you can install directly and quickly renumber your rooms however you need to.

http://labs.blogs.com/its_alive_in_the_lab/2011/02/march-adn-plugin-of-the-month-roomreumbering-for-revit-now-available.html