Hi Josh -
Well, it depends. First question: have you figured out how they got in the wrong workflow and corrected it? (check conditions, categories, etc)
Next question: does it matter if the history reflects that the files were in the wrong workflow? If no, then you can use New Workflow Link to transition a document from one workflow to a specific state in the desired workflow. If yes, then copy the files to a location outside the vault, destroy the ones in the vault and check them in again (making sure they go into the correct workflow).
Your VAR should be able to provide you some guidance.
The workflow link is what we were looking for thank you for the input.