Stopped all the collectors and restarted the collector where new certificate was added and saw the below errors in the logs.
[DEBUG] [Connection Helper 2] [Manager.IncomingConnectionListener] Incoming Connection threw exception. This may happen normally when a Workstation logs in: javax.net.ssl.SSLHandshakeException: Received fatal alert: certificate_unknown
Made the change in the certificate with root and imported the agent side certificate in a single certificate. After that, all is working fine in collector.
May have to add the cert to the keystore and truststore. (And Java keystore) to resolve this.