It is possible to do this, but it takes a little manipulation. SMSAP will check to see that the host where the profile resided is still available. If it does not ping, then the operation will fail. So if the host is not up and running, simply put an entry in the /etc/hosts file with the hostname for the old server and an IP address of any machine that is running.
After those are available, you can delete the profiles without a problem.