What is difficult about renumbering DNS entries? You DO refer to your
websites with hostnames don't you? The nameservers themselves are a bitch
(since you break all the clients unless you're using dhcp) to renumber, but
none of your other services should have problems.
What protocols (besides FTP) are you referring to? FTP translators are
common enough, and I am not aware of any other user application protocols
that transmit IP addresses.