Navigraph AIRAC updates are for add-ons to FS (FS9, FSX and P3D) and do not update FS itself.
So whilst the add-ons will show real life data, FS may well be out of date for certain airports. This could include changed runways, ILS frequencies etc.
There are references in this forum and others to add-on scenery and AFCAD editing programs to change data in the FS databases. These are on a per-airport, manual basis.
You may also find suitable Flight Simulator navaids updates at http://www.aero.sors.fr/navaids3.html .