In my game the player puts things in runtime on the map, the way I do is set collision to none during the time user is placing it and as soon as user presses confirm to place it places the object there and changes its collision to block and overlap
but doing so has no effect on nav mesh what so ever , but if I place the object with collision set to blocked from start it affects the nav mesh but is against the game logic.
In short changing the collision settings of a skeletal mesh in runtime does not causes it to interact with navmesh, while doing same in a static mesh works