You can go into the mp_Sites table and change the IsServerAdminSite flag to true to make a site a master site and false to make it not one. You should not be able to delete the site if isserveradmin is true and you should be able to delete it if it is false. Be sure to touch web.config to clear the cache so it sees your change.
Also be sure to backup first in case anything goes wrong.
If there are more than 2 sites the one with the lowest siteid should ideally be the master site because it will be the default site if no other sites match the hostname or folder name.
Hope it helps,