Was there any alias or load balancer used for web applications in the initial configuration?
If yes, you will have to update those entries manually.
For hyperic.keystore, yes it has to be generated again with new certificates. I think the steps are documented in the guide you have shared.
As part of updating hostnames there is a file generated for some manual changes which has some steps to be done in the agent configuration, have you performed them?
There is a manual step on the compute server where EVM datamart is hosted to change the hostname manually in the sasev.properties file. Have you performed that as well?
I had a similar issue after cloning of environment and it got resolved after all the required manual steps and flushing data folders.
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