... cloning of "mdServer-000006.vmdk" came back with an error, ...
Did you replace the missing file prior to starting the cloning process?
If you did, please provide details about the error.
Unless the missing file can be restored from a backup, the data that was stored in this file is fone (~4GB).
However, it should at least be possible to create the mentioned clone, so that most of the data can be restored.
From what I saw in the file that you've provided, the important snapshot chain is:
base.vmdk -> 000002.vmdk -> 000007.vmdk -> 000001.vmdk -> 000003.vmdk -> 000006.vmdk
It looks like you reverted to snapshot 000003.vmdk (mybe while troubleshooting the issue), and that's why you also have a snapshot 000005.vmdk, which also has 000003.vmdk as it's parent.
A clone of 000006.vmdk will contain all of it's own, as well as it's parent's data (except for the data in the missing file).
André