Microsoft published a new System Center Virtual Machine Manager 2008 solution; "The issue is one where on SCVMM 2008 or 2008 R2, duplicate VMs may appear in SCVMM Administrator Console. In this scenario, one of the duplicate VMs has a Missing status, and the other VM has a different status. If you try to delete missing VM, you may receive: Error (802) – The VM file vmname.domain.local is already being used by another VM," explains Microsoft in KB983839.
To resolve: Close SCVMM Admin Console; Stop SCVMM service (VMMService.exe) on SCVMM server; Make full backup of SCVMM database; Install Microsoft SQL Management Studio Express on computer that has SCVMM database; Run SQL Server Management Studio Express, select SCVMM database, and then run SQL script; This script deletes all missing VMs that've a Missing status from SCVMM database; If script was successful, you see following output: Commands(s) completed successfully. After script has finished, restart SCVMM service (VMMService.exe) on SCVMM server, and then open SCVMM Administrator Console to verify that missing VMs were deleted.