2004944 - How to continue system upgrade when java stack cannot start due to error "agent library failed to init: instrument"

During upgrade/migration of SAP system, java stack does not start up. And could see below errors in folder usr/sap/<SID>/<xx>/work.

dev_server0:

J  Error occurred during initialization of VM
J  agent library failed to init: instrument
J  Event buffer was not initialized yet - no flight recorder available

std_server0.out:

Error opening zip file or JAR manifest missing : /usr/sap/DAA/SMDA97/SMDAgent/applications.config/com.sap.smd.agent.application.wily/BytecodeAgent/ISAGENT.9.1.0.2-2013-01-18/wily/Agent.jar
Error occurred during initialization of VM
agent library failed to init: instrument
Event buffer was not initialized yet - no flight recorder available

• Release Independent 
• SAP NetWeaver

Agent.jar, SMDAgent, -javaagent, -Dcom.wily.introscope.agentProfile, IntroscopeAgent.profile, agent library failed to init: instrument, Error opening zip file, Error occurred during initialization of VM, -Dcom.wily.introscope.agent.agentName , KBA , XX-PART-WILY , Introscope by CA Technologies , BC-JAS-COR , Enterprise Runtime, Core J2EE Framework , SV-SMG-DIA-WLY , Solution Manager / Introscope Integration , Problem