Clone server has two endpoints running, one for web browsers and other clients to talk to (normally port 14145, and HTTP by default, but both are configurable), and a second one reserved for agents (port 14146, and always HTTPS).

You need to use the agent endpoint with SERVERURL - e.g. https://mycloneserver:14146.

• On the affected agent machine, navigate to C:\ProgramData\Red Gate\SQL Clone Agent and open settings.json.
  • (On non-Windows 10 or Server 2012 installations, this will be in CommonAppData for your OS.)
• Update the ManagementService->Url field to port 14146, and make sure the protocol is HTTPS.
• Using services.msc, restart the SQL Clone Agent service. It will re-read the settings file and attempt to establish a connection.