Hi Amit,
Can you check the below links it may help you. Also please check roles are generated and user comparison is completed.
http://scn.sap.com/community/it-management/alm/solution-manager/blog/2014/05/27/decommissioning-
a-managed-system-from-solution-manager-71-sp11
Delete_Managed_System - SAP Solution Manager Setup - SCN Wiki
Thank you.
Regards,
Jaskirat Sing