That's definitely not normal. Did you check whether the files show up in a Lost+Found folder?
If you cannot find, or recover the files, you may create a new temporary VM with the current VM's original virtual disk size, copy the missing extents from the new VM, and rename them, this should at least allow you to access the virtual disk again. Make sure that you create a snapshot after replacing the missing files, and before powering on the VM, so that the remaining files won't get modified in case something doesn't work as expected.
André
