Hi Utkarsh,
When you get the following messages in WAAE 11.3.5 release:
"Return values from dual database writes disagree. Databases may no longer be synchronized."
the solution will be to run "reconcile" scripts available under $AUTOSYS/dbobj/ORA directory.
By default the "reconcile" scripts are available under the following location:
/opt/CA/WorkloadAutomationAE/autosys/dbobj/ORA
I will be helping you to apply the solution through the case you have opened at CA Support.
Thanks,
Roya