Why not store this as one whole document. I understand that certain sections need to be updated, but ... The 2090 Document Server has the Editor capability. With this feature you can select ranges of pages to be deleted and then simply added by scanning in the new updated pages. Plus once you enter the settings for this entire job, they are kept, regardless of how you delete and add pages.
But perhaps the greatest way to impact their productivity work flow would be to connect this system. That way an operator can edit jobs from their desktop. This can be done several ways, DTB, Velocity (if EFI) or with TR Systems.