I encountered this problem, but with your note, have been able to fix it in ~60 seconds.
On the affected VM, download the .vmx file to a local machine where you can use notepad, textpad, etc.
Towards the top of the file, you will notice the drive mappings and SCSI IDs used by the VM that are pointing to the wrong files. At the bottom of the file, you will notice the correct SCSI ID and path pointing to the VM's correct swap file location. Cut and paste the entire path and file name and replace the bogus path in the drive entry(ies) at the top of the file.
(To be clear, only paste the appropriate amount of filename, not replacing the entire thing, but you should be able to rebuild the proper paths with the information from the swapfile path.)
Save, upload back to the VM directory, power on. VM is now useable again without re-cloning.
-Phil
