The protected node module has global settings found under:
Administer » Site configuration » Protected node
The page starts with statistics to let you know how pages are protected on your website. All the counts include published and unpublished content.
That way you can come back to your previous version if anything goes wrong. So far, no one told me that they had a problem upgrading. Although version 2.x did not have any schema, the new module may modify nodes and generate incompatible tags.
Version 3.x has a new theme() scheme. It is much more powerful has it allows you to create your own header numbering, etc. However, if you already had a theme() overload in your theme, it will stop working until fixed.
Please, in this case, make sure to upgrade on
Global settings are found under Administer » Site configuration » To do list (admin/settings/to_do).
Only To Do List administrators can edit the Global Settings.