Before delete the folder please take a clone of the VM.
Once you take a clone of the VM ,
1, Go the orginal VM setting , note down all disk datastore path and SCSI # .
2, Remove all disks from the VM ( Dont delete the disk) and click finish
3, Again go the setting and add the disk one by one and finish.
4, Now try to power on the VM & check the status of the VM
5, If everything fine then u can delete the folders as you mentioned.