Hello. Installation of the airacs via Navigraph Navdata Center eliminates VOR, ADF, ILS and procedures in the simulator.
your scenery-content file is messed - please follow EXACTLY all the following steps from the FAQ and all should be back - that´s not a navdata issue, it´s sim related due the none-ordering/prioritizing of the sceneries in the content-file, sorry. Happens from time to time …
But again, when you follow these steps, it should be fine: