After changing the "hostname" in "agentparm.txt" file to the new scheduler name, 

the new scheduler name is over-written by the old scheduler name.

Release : 11.3.6

Component : CA Workload Automation AE (AutoSys)

The encountered problem is related to the old scheduler "using the same instance codes",

running and submitting jobs to the "same agent".

Problem was Not encountered anymore after stopping and decommission of the old scheduler.