Simply copying the files should have worked fine. Once you have the VIDEO_TS folder ripped (and deCSS’d) to your HDD then you should be able to treat them just like any other files/folders.
Sounds to me like there is some other problem here; have you copied any files successfully to the new drive?
If all the .VOB files are filled with zeroes, then it sounds to me as though the file allocation table entries (holds the file name, size, date etc.) were created successfully for the files, but the actual contents of the files failed to copy across.