It has been found to be a cosmetic issue that does not affect the actual VM metadata restore. This finding can be verified by taking a metadata backup using the xsconsole, deleting a VM (not the disk since this is not part of the metadata and it is irrecoverable) and then restoring the metadata backup. The deleted VM should be restored and work normally. 

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Problem Cause

Currently under investigation, contact Citrix Support if you want to know the status.