First, you'll want to move it to at least Server 2012 R2. Server 2008 R2 is officially unsupported on the next major update for all Orion products. You get a warning today when installing that it's going to be deprecated.
Second, Once you have the new server OS running, I'd install the new APE on it which should give you a 30-day evaluation. Once your Orion recognizes the new APE just move everything on the old APE to the new one for monitoring. If you have ACL's in place then you'd have to update that with the new IP of the APE or just have some downtime while you re-provision the IP.
Once the old APE has nothing on it then open up the license manager and deactivate the key. Then once it shows as available on your customer portal then apply it to your new APE.