Regardless of which method you use (MSFS or Navigraph) it is important to actually load the Scenery Library from MSFS into LNM. This will ensure your NAVDATA and scenery are in sync (gate to gate).
This ensures airports, taxiways, parking, etc… are all up to date with your Scenery, etc…
From the top, select “Scenery Library” → “Load Scenery Library” → “Load”
This will scan your MSFS install (as well a your community folder, so if you use an app like Addon Linker, ensure all addons are enabled so it can include those as well).
Once it’s done, select “Use Library”
You will see an error for encrypted airports it cannot read, this is okay.
https://www.littlenavmap.org/manuals/littlenavmap/release/latest/en/SCENERY.html