@dhananjayan02​ 

You may want to refer to this KB article: Reconcile is not running or stuck in progress state as killing or terminating an abnormally long-running reconciliation job in FlexNet Manager Suite (FNMS) involves the Batch Scheduler, worker executables (ComplianceReader.exe), and active SQL Server transactions, i.e. properly handling of all three layers.

Thanks,

John Sorensen