It may not be empty. Depends on the filesystem and what has happened. Just because the pointers to those files are gone doesn't mean that the bits have been erased. You could zero out the empty space.... but be careful or that will expand the VMDK to full size.
That is what I did, but I knew there was enough space for the entire disk to expand out.
I think that that is becoming less and less true. Quirky environments are becoming less and less the norm. The need to install locally is rapidly going away. There are still things that get installed locally but the variety and commonality is dropping at a prodigious pace and the isolation of programs is getting to be quite good.