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Not sure if it will help or not, but when I ran into a similar issue, it was because I did not chain my certificate properly. I used an online SSL checker (e.g. https://www.ssllabs.com/ssltest/) to help me get it properly chained. After correcting the certificate chain and re-applying it, downstream clusters re-joined the Rancher manager instance on their own. This might not be your issue, but it helped me in the past.

So, i have figured out that the base64-encoded certificate in /var/lib/rancher/agent/rancher2_connection_info.json is not correct and changed when following the guide. Hence the provisioning or alteration of resources fails as it somehow gets the wrong certificate from the cluster. Not sure how to proceed. Does anyone know what sets this value to start with?