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Sorry that you've had a bad experience with the product. This specific problem has caught a few administrators out before so...
I think here is as good a point as any to explain a little more of the VirtualCenter interaction with VDM 2.0/2.1. VDM uses VC for creation and deletion of VMs as well as power management, it also uses it to pass configuration information to the VDM agents running on the VMs, and keeps track them by their vmpath. For those that don't know what that is, it's depicted fairly accurately by looking at the folder structure in the "Virtual machines and templates" view in the VI client.
VDM 2.1 will happily keep track of VMs when moved between hosts,clusters,resource pools and datastores, but requires that the vmpath remains constant. Make sure to pick this path correctly the first time, if you need to change it you will either have to manually make changes to VDM's database or re-add them. You can spot when VDM has lost track of a VM by the following log message:
Not found: /my-folder1/my-datacenter/vm/my-folder2/my-folder3/my-vm1
VDM will eventually remove the VM entry if it doesn't hear back from the agent on that machine. Note that if you keep the VMs in the same place this will never be an issue, and we're aware that it can catch people off guard so improvements will be made around this area in the next major release.
Mike
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On a related note: starting with VDM 2.1 we include the vdmexport tool, which is in the server bin directory - this allows you to do a full backup of the VDM environment (server settings, pools, entitlements) should something go wrong. Again, this tool has not been well advertised but I strongly recommend that all customers use this to do regular backups of their environment so that if data is lost (I know I've accidentally deleted the wrong VM or pool when testing) it can be restored again. Simply redirect the output to a file as below:
vdmexport >c:\daily-backup.ldif
Steps for restoring the data are included in the file header.