Only one thing, but an important one - we edit the content.xml file to disable the stock navdata and to place our navdata at the correct priority wrt the sim and sceneries.
Removing the navigraph-navdata folder only will keep a content.xml file with stock navdata disabled and a reference to a non-existant Navigraph folder.
Navdata Center restores the content.xml file during uninstall.
Deleting content.xml and letting the sim recreate it is a dirty way to restore the stock data without using Navdata Center.
Using the Microsoft/Zendesk guidance of manually clearing Community will unfortunately leave you with no navdata at all.
Stephen