Virtual disks consist of 2 files, a descriptor/header .vmdk file, and the data .vmdk file (flat.vmdk, delta.vmdk, or separse.vmdk).
The latter are usually hidden in the Datastore Browser, and only show up in case the descriptor files got lost, or corrupted. However, depending on what happened, it should be possible to recreate the descriptor files.
To get an overview, please run
ls -elisaR > filelist.txt
from the affected datastore's root folder (i.e. /vmfs/volumes/<datastore-name>/), and attach the resulting filelist.txt to a reply post.
André