I upgraded Melodyne as instructed (opened Melodyne in a Sonar project) but CCC still lists the old version. 

Once any version of Melodyne is installed, updates and upgrades are handled directly from Celemony. Why not hide the Melodyne line item in the Command Center by right-clicking on the item and select "Hide this product."

If it is an item to be listed by the CCC then it needs to be able to detect what version is installed.

I do not believe Cakewalk has officially released the version of SONAR with Melodyne 4. I am not sure what to expect from the Command Center when a product is updated to a version newer than the program knows about.

That's correct. Your new serial number and info will be available on the Celemony site. You won't see it in Command Center but it is working in SONAR so you can see the update and download it from Celemony. In the next update, we'll be putting in new installers and customers who purchase at that point will see new installers and serials. But anyone who renews won't get a new serial number or installer since they can get the update way more easily through Celemony.