The changes are to ensure more reliable data is being pumped through to the databases.
Obviously the database on your local machine is a static, and a software update will be needed to ensure changes are picked up or a refresh proceadure added.
This is the first stage, so we can ensure reliable data is being passed through and server load is fine before updating the software.
However yes, a clean of your NavData database would force it to get fresh data from the server for all aircraft. For customers who don't do this only new aircraft you pick up will be checked using the new routines.