What I've done in the past in such case, is to move the .vmdk files (note there are two of them for each virtual disk) from the command line. After I moved the files, I also renamed them using the vmkfstools command to avoid confusion.
Sample:
cd /vmfs/volumes/datastoreX
mv ./oldfolder/old-vdiskname.vmdk ./newfolder/old-vmdiskname.vmdk
mv ./oldfolder/old-vdiskname-flat.vmdk ./newfolder/old-vmdiskname-flat.vmdk
cd newfolder
vmkfstools -E old-vmdiskname.vmdk new-vmdiskname_1.vmdk
(Caution: Make sure that the target filenames aren't already in use, i.e. that you don't overwrite existing files!)
André