If you mean the keys such as password for SSL and others for clustering from inputs.conf and server.conf those are based on the $SPLUNK_HOME/etc/auth/splunk.secret. The Splunk instances need to all share that splunk.secret for the values to decrypt properly. If you did not have splunk.secret in place before starting Splunk the first time you could have to test to make sure you don't miss copying all possible files that are encrypted using it.
I often will take splunk.secret from a cluster master and place it on cluster nodes before starting them the first time. This ensures all cluster members share the same secret and configs can just have the encrypted value in the files.
