Dan, you can use the licences fine. the issue will be the SRP, you cannot have an SRP used on more than 1 machine, the 2 servers will fight to be the one "logged in" with that SRP and auth code, after about 60 seconds the SRP will be locked out and unuseable for about an hour or 2.
Is your new Exchange org in a different domain to the old one.
You did not mention it, and you can join NT domain servers to an Active Directory, and you can also add old echange 5.5 orgs to Active Directory domains and migrate gradually, exactly what path are you taking here ?
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