Tested versions

• Reproducible in latest master (eee39f0)
• Not reproducible in 4.4 beta 2

System information

Godot v4.4.beta (eee39f0) - Windows 10 (build 19045) - Multi-window, 2 monitors - Vulkan (Forward+) - dedicated AMD Radeon RX 580 2048SP (Advanced Micro Devices, Inc.; 31.0.21921.1000) - AMD Ryzen 5 3600 6-Core Processor (12 threads)

Issue description

When you have two or more scenes open with unsaved changes and attempt to close the editor, selecting Don't save lock the engine from be closed or restarted.

After select Don't save these three errors will appear:

ERROR: Can't add child '@ConfirmationDialog@8238' to itself.
   at: (C:\Users\Matheus\Downloads\Godot Source\scene/main/node.cpp:1652)
ERROR: Condition "!windows.has(p_window)" is true. Returning: -1
   at: DisplayServerWindows::window_get_current_screen (platform\windows\display_server_windows.cpp:1959)
ERROR: Condition "!is_inside_tree()" is true.
   at: Viewport::_push_unhandled_input_internal (C:\Users\Matheus\Downloads\Godot Source\scene/main/viewport.cpp:3338)

And any new attempt to close/restart the editor or close a scene will throw this error:

ERROR: Condition "!is_inside_tree()" is true.
   at: Window::popup_centered (C:\Users\Matheus\Downloads\Godot Source\scene/main/window.cpp:1794)

Bisecting points to #102070 as the culprit

CC @ryevdokimov

Steps to reproduce

1. Open two scenes at the same time
2. Do any modification in both scenes but don't save
3. Try to close/restart the editor
4. In the confirmation window, choice Don't save

Minimal reproduction project (MRP)

N/A