If you change the folio manually using the InDesign function (Layout>Numbering & Section options…) or you add more pages in the document via the InDesign Pages Palette, the manual alterations are honoured and saved providing you have the InDesignPlugInEnabledImport option set to true.

If this option is set to false then an error will result on saving the document:

In the example above, page 2 had its folio altered by a user with the false setting and attempted to save the document.