YES! The original workbook and the users' workbooks (even after they have started completing them) are linked and identical. Any changes you make to the original will be replicated in the users' versions. This has the benefit of enabling you to fix small errors and drip feed elements and/or pages over time. However, it does mean that anything you remove will also be removed from the users' workbooks. If you need to start making changes to the workbook for the next cohort of students you need to COPY the original and make the changes to the copy. This will then not impact on the original or the students who are using the original. It is a good idea to get some naming conventions worked out so that you can keep track of the various versions of your workbooks.
This Help topic explains the concept of how Worbook resources utilise Live Links.