From what I've seen, another problem with direct file extraction is that references are not corrected in Windchill files. Not only are the filenames hashed, but the names internal to the files are bounced against a table. That way, when you have 5000 assemblies that refer to a part, and you rename the part, Windchill doesn't have to alter all 5000 files. It just keeps track of the change and fixes the name references when you ask for the file. I'm not even sure it does this when files are copied to a workspace; it may delay it until the file is opened.
If time is not a great factor, a script that just opens them in Pro/E or Creo directly and then does a backup may be your best bet. Scripting the CAD tool is pretty easy, and you get the benefit of finding out about whether the models are any good. There's no need to add to workspace as the link to Commonspace will be used by the CAD tool to retrieve items as required.