tusharkotwal, Welcome to McAfee Community.
First thing I would check is permission setting of the epo user account that is trying to delete a system. Please review your permission settings in "Permission Sets" under User Management category.
Is that an active system on the network? Can you possibly try to reinstall agent, make sure it communicates with ePO, and then try deleting from system tree? What is the last communication time?
Permissions are proper as its main admin account and systems entry is old means duplicate entry so no use of deploying again agent.