Something really nasty happened to me when I was working on storage vmotioning a ton of VMs onto new datastores. Basically I was not paying attention and tried to manually remove a Virtual Machine from the datastore using the datastore browser. This basically wiped out the .vmx and.vmdk files, leaving only the flat.vmdk file which could not be removed as thankfully it was in use.
Anyway once I had realized what I had done, and got my mini panic attack out of the way, I found the following kb from Vmware. Reference it here.
In order to get your VM back up and running you must create a matching .vmdk file to go with your flat.vmdk file. You do this using the command below. Note that you must know the size of your flat file in bytes.
# ls -l vmdisk0-flat.vmdk (gives you size in bytes)
Create a new virtual disk/vmdk file and a temp flat file.
# vmkfstools -c 4294967296 -a lsilogic -d thin temp.vmdk
Now delete the temp flat file that you just created.
# rm temp-flat.vmdk
Rename your temp.vmdk to match the name of the flat.vmdk from your vm
mv temp.vmdk vmdisk0.vmdk
Now vi the .vmdk file and point it to the flat file at the line below. You may also need to remove the last line if you did not use thin provisioning on the original vm.
# Disk DescriptorFile
# Extent description
RW 8388608 VMFS "vmdisk0-flat.vmdk"
# The Disk Data Base
ddb.virtualHWVersion = "4"
ddb.geometry.cylinders = "522"
ddb.geometry.heads = "255"
ddb.geometry.sectors = "63"
ddb.adapterType = "lsilogic"
ddb.thinProvisioned = "1"
Now you can go through the process of creating a new VM via VCenter, only instead of creating a new virtual disk, you use the vmdk file that you just created. You should then be able to power on your rescued VM.