Scene instantiated in another thread breaks NavigationRegion3D

[joelgomes1994]

Tested versions

• Reproducible in: v4.5.stable.official [876b290], v4.6.dev.custom_build [0f3e975] (build from master)
• Not reproducible in: v4.4.1.stable.official [49a5bc7]

System information

Godot v4.5.stable - Windows 10 (build 19045) - Multi-window, 2 monitors - Vulkan (Forward+) - dedicated NVIDIA GeForce RTX 4060 (NVIDIA; 32.0.15.7652) - AMD Ryzen 5 5500 (12 threads) - 15.87 GiB memory

Issue description

I am developing a stage-based game that instantiates each new stage in a separate thread. I noticed that after updating from Godot 4.4 to 4.5, enemy navigation stopped working properly, so I reverted my project back to 4.4.

After some investigation, I discovered that it is possible to fix this with a hack in GDScript by disabling the NavigationRegion3D and re-enabling it some time later, like this:

@onready var navigation_region: NavigationRegion3D = $NavigationRegion3D

## HACK: Disables and enables navigation region after a short delay.
func refresh_navigation_region() -> void:
	navigation_region.enabled = false
	await get_tree().create_timer(1.0).timeout
	navigation_region.enabled = true

Still, I believe this is unintended behavior.

2025-10-02.13-56-49.mp4

Steps to reproduce

• Instantiate in another thread a scene containing a NavigationRegion3D and NavigationAgent3Ds
• Add the scene instance to the scene tree

Minimal reproduction project (MRP)

The project is the one shown at the video above. You can enable and disable the said 'hack' I talked about in the level_manager.tscn scene.

test-navigation-spawn.zip

[smix8]

Cant reproduce that issues even with your "hack" code removed.

You likely have timing issues because that thread use is broken and unsafe. It is continuing the await spaghetti before the thread task is even finished and joined back with the main thread.

In Godot 4.5 regions are cached. So if you create them broken they stay that way until an actual extra update call, e.g. an enabled toggle, forces them to build a new iteration.

The reason you likely did not notice how broken that thread use already was is because in Godot 4.4 any map change did rebuild all the region iterations again, so basically any modification you did to the navigation map or regions fixed all the prev broken changes.