I have a Windows 2008 server running right now in production (luckily). What seems to have happened is we were upgrading from ESX 4 to 5.x and adding more hard drive space to the two ESX 5.x servers we have. When doing so we moved a VM to the second ESX box to do the upgrade then moved it back afterwards to upgrade that one from 4 to 5 and add hard drive as well. I do not know exactly how, but not all the vmdk files were migrated back to the server after upgrade and it came up and is running so we did not notice right away. Then when trying to do a snapshot for an upgrade to components of the 2008 server it failed with unspcified file not found.
I did some research and it would seem one of the files is missing ,<server name> 000007.vmdk out of 12 vmdk files is gone. So we have been running in snapshot <server name> 000012.vmdk and collecting all these files and cannot consolidate or take a new snapshot. (we are talking a long time now) so I have read you can recreate a enpty file and then consolidate, but in never doing so myself do not feel confortable without some guidance as the information I found is for ESX 3 and we are running ESX 5.x
I have attached the log file that shows the error and my attempt at fooling it by recreating blank VMDK file.
To me this looks more like a corrupt .vmsd file. To verify this please enable SSH on the host and use e.g. WinSCP to download all the VM's descriptor .vmdk files (the files with only a few hundred bytes in size), the .vmsd file as well as the .vmx file. Then compress/zip these files and attach them to a reply post.
Btw. .vmdk the file names (snapshot names) do not necessarily have to be in an ascending order.
To me this looks like some "old" issues with the VM are causing this error message. There's a reference to an...000007.vmdk in the .vmsd and you also have a 000011.vmdk which does not seem to be in use (looks like a manual copy of the 000010.vmdk). What I would suggest - assuming you don't need/want any of the existing snapshots anymore - is to properly shutdown the VM, delete the .vmsd file and then reload the VM (see http://kb.vmware.com/kb/1026043). After this you should be able to create a new snapshot - to enable the "Delete All" button in the Snapshot Manager - and then use "Delete All" to consolidate/merge the snapshots into the base disk. You can either delete the snapshots with the VM powered on or off, but remember that you cannot power on the VM until the deletion finished, if you decide to do this with the VM powered off!
Due to the number of snapshots and their sizes, it might take some time to do the job, so please be patient and ensure no new snapshot is created (e.g. through a backup application). Unless I'm mistaken, the 000011.vmdk is obsolete and will remain in the VM's folder after deletion. In this case ensure the .vmx file points to the base virtual disk and it does not show up in the latest vmware.log file before you delete this file.