SSH to ESXi connected to datastore and navigate to the datastore which it resides and run command
rm -r <foldername>
If it is not deleted with the above try adding f
rm -rf <foldername>
You know for sure it is unused?
can you please run below command from the vmdk directory and share output
vmkfstools -D xxxxxx.vmdk
vmkfstools -D xxxxxx-flat.vmdk