Thanks You everyone for your help on this.
The root cause of the issue is:
Vendor team for SAP upgrade project had updated the SAP management console without letting us know. Which caused some discrepancy on netweaver AS java and stopped message server.
Since I was not aware about this change so I was doubting on Nakisa file which was recently deployed.
When I was trying to start the JAVA using SAP MMC it was showing me message server in yellow status.
Now the issue is, if I start CI & app instance separately, it's working fine but message server in yellow status.
If I start whole system (CI & app instance) together, SAP MMC reads message server as yellow status and not starting app instance (if I start manually, it works regardless of message server status).
I used sap note:
1624464 - SAP MMC shows Message Server in yellow and with status "Running but not responding"
Still same issue.
Do you have anything to suggest on this?
Thanks,
Hardeep