I did not do a search for technote for this, but what I think is that you do not need to decommission at all.
With NetBackup 6.x, all the volume/media catalog information is stored within EMM database on the EMM server.
Unless that media server is also an EMM server (normally I see most people configure EMM server on their master server) there will be nothing you'll really need to do.
Whatever you do, don't forget to take a full filesystem backup on that media server first, and keep the tape in safe place.
Then just rebuild the server - install OS, give it the same hostname and IP address as before, install NBU with same license and specify same master name, etc.
EMM server will continue using the same storage unit fine, because the hostname remains the same.
However, if the rebuild is going to take time, then you might want to temporarily delete the storage unit for that media server - just to avoid any unexpected issues that the job scheduler and resource broker might face.
Well, it's best to finish the rebuild process between the backup windows - so your scheduled backups do not have to skip the night's backup.
Abe