Navigraph AIRAC updates are for add-ons to FS (FS9 or FSX) and do not update FS itself. FSC derives its runway data from FS when you run FSCDbManager.
Hence at certain airports FSC may show different data to the add-on FMC’s. This could include changed runways, ILS frequencies etc.
There are references in this forum and others to add-on sceneries or AFCAD editing programs to change data in the FS databases. These are on a per-airport, manual basis.
If you update FS using an AFCAD program or add-on scenery, make sure you run FSCDbManager again after updating FS. Then your FSC airport data and add-on SID/STAR/APPR’s should match.