I am moving a CharacterBody3D with a NavigationAgend3D. If i block off the path completely (i.e. with a big enough StaticBody3D) my CharacterBody3D walks up to that obstacle and stops. Now i want the StaticBody3D to resume it’s way to the target location once that obstacle has been removed. However, if i remove the StaticBody3D and its parent (MeshInstance3D) and then call bake_navigation_mesh the area does not seem to be updated.

The nodes get deleted from the SceneTree and if I do this manually in the Editor the NavigationMesh gets updated correctly.

This is my scene:

And this is the script

extends CharacterBody3D

var movement_speed: float = 2.0
var movement_target_position: Vector3 = Vector3(-10.0,0.0,10.0)

@onready var navigation_agent: NavigationAgent3D = $NavigationAgent3D
@onready var navigation_region_3d = $"../NavigationRegion3D"

func _ready():
    # These values need to be adjusted for the actor's speed
    # and the navigation layout.
    navigation_agent.path_desired_distance = 0.5
    navigation_agent.target_desired_distance = 0.5

    # Make sure to not await during _ready.
    call_deferred("actor_setup")

func actor_setup():
    # Wait for the first physics frame so the NavigationServer can sync.
    await get_tree().physics_frame

    # Now that the navigation map is no longer empty, set the movement target.
    set_movement_target(movement_target_position)

func set_movement_target(movement_target: Vector3):
    navigation_agent.set_target_position(movement_target)

func _physics_process(delta):
    if navigation_agent.is_navigation_finished():
        return

    var current_agent_position: Vector3 = global_position
    var next_path_position: Vector3 = navigation_agent.get_next_path_position()

    velocity = current_agent_position.direction_to(next_path_position) * movement_speed
    move_and_slide()
    for i in get_slide_collision_count():
        var collision = get_slide_collision(i)
        print("I collided with ", collision.get_collider().name)
        var obstacle = collision.get_collider()
        print(obstacle)
        var mesh = obstacle.get_parent()
        for n in mesh.get_children():
            n.remove_child(n)
            n.queue_free()
        mesh.queue_free()

        navigation_region_3d.bake_navigation_mesh(false)
        print("Baked navigation mesh")
        set_movement_target(movement_target_position)

    

And this is the scene without obstacle (removed and baked again in the editor):

What am i doing wrong?