If I understand your scenario properly, you are using the Deployment Wizard to upgrade your existing agents.
Firstly, let me say that Software Delivery is the preferred method for upgrading agents. Unless this is an Asset Management-only installation of ITCM, you should leverage Software Delivery to upgrade your existing agents.
The Deployment Wizard is better suited for new agent installs. Although it is capable of upgrading agents. Just Software Delivery is much smoother and uses normal ITCM ports, than the requirements and moving parts associated with the Deployment Wizard.
Secondly, once an agent is upgraded, it should register automatically (caf register). The agent will register with its scalability server. From there, the Engine running the Collect Task associated with that Scalability Server will pickup the registration message, and update the agent details in the database.
The agent will register automatically, once per day. It will also register anytime the CAF service starts up, a user logs in, the system reboots, or if any network address changes. So registration is both scheduled and event based. You can also manually trigger a registration with "caf register".
Since upgrading the agents, what does a "caf setserveraddress" return? Is it the scalability server you expect? And if so, is the collect task for that SS linked to an engine in DSM Explorer?