You should not just delete your community folder. If you simply remove the navigraph-navdata folder, you will end up with having no navdata in the sim at all (because your sim is then pointing to a non-existing navdata folder, hence you see no navdata).
To remove Navigraph navdata you must follow the uninstall procedure: FAQ - MSFS Uninstall the navdata (revert back to the stock data) - FAQ - Navigraph
Now, you recovered by reinstalling the Navigraph navdata, so I guess you are fine, but for future reference follow the procedure above if you want to revert to stock navdata.
Stephen