First of all, you are probably using version 1.x (or at least were using it when the files in question were encrypted). There was a known issue there when this could happen if a file was on a removable medium and it was removed without using the ‘safe removal’ feature of Windows.
Since the files are literally empty, zero bytes, there is nothing there. I am sorry, but the data is lost and needs to be recovered from backup copies. You can thus delete them, there is no reason to keep them.