It would be helpful to be able to remove a (missed) waypoint from the current route in Android Auto. If this is already possible, I have missed the trick and would be thankful for tips on how to do that. The current procedure which is (at least for me) required to remove a waypoint while navigating is the following:
disconnect the mobile from Android Auto
remove the waypoint (unchecking is not sufficient!) from the route
reconnect the mobile to Android Auto and
restart the navigation
This procedure is by no means doable without co-driver or parking the car.
I have noticed this also, when setting a new destination, old waypoints remain in the route list. It would be nice if it asked whether to keep or clear the existing waypoints. Also, in Route Info under the ... dropdown, the "Delete Waypoints" can be misleading, it should perhaps be "Clear Waypoints". Delete could imply deleting them from your favorites or whatever.
As it is now, go to Route Info first and delete waypoints (or all) before setting your destination, or in the middle of navigating (having stopped for whatever), uncheck the passed waypoints.
I can't see the problem. Set Your new destination, then go to route info and simply choose remove waypoints in the ... menu. Everything between start an destination will be removed without affecting favorites or saved routes.