Solution to SCVMM Error (402) "Library server is not associated with this Virtual Machine Manager server."
1. go into the VMM database to the table tbl_WLC_VObject, and change the ObjectState field of the problem VM, which probably has the value 104, to value 1
** At this point, i went direct to the table and edit the value manually. Of course I did this because this I a Lab environment.
update dbo.tbl_WLC_VObject
set ObjectState = 1
where Name = '<VM name>'
2. in VMM admin console, you're VM will now have the status missing, now just delete the VM and it's gone.
Answer found here on : --> https://social.technet.microsoft.com/Forums/en-US/virtualmachinemanager/thread/872034ba-3545-4431-b9f6-07ee8c65188b