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You need to lock the regions except where you want the users to intervene and change values. So put your scriptable objects in a different area, and define all variables in a separate area that you can lock and even hide. We do this with student content, and in our high school product, StudyWorks.
The other method is to create your files as an electronic book. Anything in an electronic book can not be change permanently by the user. The Mathcad Resource Center is an example of a Mathcad electronic book. Mathcad 2000 contains authoring instructions for creating electronic books. If you have an earlier version of Mathcad, you can find instructions posted on our website.