I've set up an AppEngine account using Google Apps Authentication and I've resigned myself to the fact that it can't be changed. But can you switch the domain that it's bound to?
UPDATE Forgot one point. We've already added users from the new domain as AppEngine administrators and we're able to log into the AppEngine console with them. But there are certain URLs in the app itself (e.g. cron jobs/task queues) that we've restricted to access by admins only. When we try to access them, we are directed to the domain-specific AppEngine page (i.e. http://appengine.google.com/a/myolddomain.com) to log in. When I update the URL to the new domain, I can log in but then I get a page saying "The page is requesting permission to access your Google account. Select an account you would like to use." And there are no options in the list to select. I can click Continue but then I'm redirected back to the login page for the old domain again.