You could just setup subdomain.com on the new server, then create a redirect from "subdomain.yourdomain.com" to "subdomain.com" when you move "yourdomain.com" to the new server. If you don't setup the redirect you will loose traffic since there will still be backlinks to subdomain.yourdomain.com and it's also in the search engine indexes.
You may be able to setup the redirect in your control panel on the new server (cPanel let's you do that). Just set it up before you change the nameservers of yourdomain.com.
qbert
