... disappearing flat vmdks ?
How do you verify this ?
If you check via datastorebrowser disappearing flat.vmdks can just mean that there is a valid vmdk-descriptorfile.
As soon as a valid descriptorfile appears the stupid datastorebrowser will hide the referenced flat.vmdk.
If you checked via putty or WinSCP you may realy have deleted the flat.vmdk by accident.
In this case - stop any further editing and renaming of files and create a VMFS header dump.
Please see my instructions here : Create a VMFS-Header-dump using an ESXi-Host in production | VM-Sickbay
If you provide such a dump I maybe able to help.
skype : sanbarrow