GoCD agents are identified on the server side by GUID values. If an agent is cloned the file containing the GUID must be removed in order to force the agent service to generate a new one. The new agent can then be enabled, as you'd do for a new agent, via the Agents page.
The GUID is recorded in
/config/guid.txt, relative to the agent's working directory. On a system with only one, default agent this directory will be
/var/lib/go-agent, this we can remove its GUID as follows:
rm -f /var/lib/go-agent/config/guid.txt