One would need to investigate whether the files are somhow still in use. Especially the .vmdk files are important, because they represent virtual disks.
Instead of deleting the files right away, you may consider to create a sub-directory, and move the files to it. If the files can be moved without error messages ("in use" or similar), and all the VMs continue to work as expected you can then delete the files.
Remember, that in case you have templates, they may only show up under VMs and Tepmlates.
André