If the folio is manually altered using the InDesign function (Layout>Numbering & Section options…) or the number of pages in the document is added to via the InDesign Pages Palette, the manual alterations are honoured and saved providing the user has 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 7 had its folio altered by a user with the false setting and attempted to save the document.