When I load the sim I have to disable and enable all Navigraph related packages in the library tab for it to show all of the Nav Data. It seems like it is not reading that the package is enabled until it’s toggled. Seems to have started after I had to safe boot the sim once. I have tried a complete uninstall of all Navigraph related content and a new content.xml file. It also resolves the issue if the 2 files related to nav data in the sceneryindexes folder are deleted before launch.
I recommend raising this on the Navigraph Forum since you’re a subscriber. They’re really good at troubleshooting.
I have brought it to their attention as well. They referred me to here, but will keep going with them.