Repository: godot
Issue: Scene doesn't update sub-scene position
Labels: topic:core

**Godot version:**
3.2.2-stable


**OS/device including version:**
<!-- Specify GPU model, drivers, and the backend (GLES2, GLES3, Vulkan) if graphics-related. -->
Linux Manjaro 20.0.3

```
System:    Host: luc-xps139300 Kernel: 5.6.16-1-MANJARO x86_64 bits: 64 compiler: gcc v: 10.1.0 Desktop: KDE Plasma 5.18.5 
           Distro: Manjaro Linux 
Machine:   Type: Laptop System: Dell product: XPS 13 9300 v: N/A serial: <root required> 
           Mobo: Dell model: 077Y9N v: A00 serial: <root required> UEFI: Dell v: 1.0.10 date: 05/04/2020 
Battery:   ID-1: BAT0 charge: 51.0 Wh condition: 51.0/51.0 Wh (100%) model: SMP DELL WN0N001 status: Full 
CPU:       Topology: Quad Core model: Intel Core i7-1065G7 bits: 64 type: MT MCP arch: Ice Lake rev: 5 L2 cache: 8192 KiB 
           flags: avx avx2 lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx bogomips: 23968 
           Speed: 1300 MHz min/max: 400/3900 MHz Core speeds (MHz): 1: 1300 2: 1264 3: 1300 4: 1300 5: 1158 6: 1043 7: 1234 
           8: 1301 
Graphics:  Device-1: Intel Iris Plus Graphics G7 vendor: Dell driver: i915 v: kernel bus ID: 00:02.0 
           Display: x11 server: X.Org 1.20.8 driver: intel unloaded: modesetting resolution: 1920x1080~60Hz 
           OpenGL: renderer: Mesa Intel Iris Plus Graphics (ICL GT2) v: 4.6 Mesa 20.0.7 direct render: Yes 
Audio:     Device-1: Intel Smart Sound Audio vendor: Dell driver: snd_hda_intel v: kernel bus ID: 00:1f.3 
           Sound Server: ALSA v: k5.6.16-1-MANJARO 
Network:   Device-1: Intel Killer Wi-Fi 6 AX1650i 160MHz Wireless Network Adapter vendor: Bigfoot Networks driver: iwlwifi 
           v: kernel port: 4000 bus ID: 00:14.3 
           IF: wlp0s20f3 state: up mac: 98:af:65:ca:57:65 
           IF-ID-1: br-4e08c797eb97 state: up speed: 10000 Mbps duplex: unknown mac: 02:42:23:2b:5a:22 
           IF-ID-2: docker0 state: down mac: 02:42:f3:b9:f9:88 
           IF-ID-3: veth58741f6 state: up speed: 10000 Mbps duplex: full mac: 02:c5:14:61:c6:b5 
           IF-ID-4: vethfe584cf state: up speed: 10000 Mbps duplex: full mac: 56:36:ce:fe:b3:ed 
Drives:    Local Storage: total: 953.87 GiB used: 187.16 GiB (19.6%) 
           ID-1: /dev/nvme0n1 model: SSDPEMKF010T8 NVMe INTEL 1024GB size: 953.87 GiB 
Partition: ID-1: / size: 921.36 GiB used: 187.09 GiB (20.3%) fs: ext4 dev: /dev/dm-0 
Sensors:   System Temperatures: cpu: 47.0 C mobo: N/A 
           Fan Speeds (RPM): N/A 
Info:      Processes: 357 Uptime: 19h 58m Memory: 15.23 GiB used: 7.59 GiB (49.8%) Init: systemd Compilers: gcc: 10.1.0 
           Shell: zsh v: 5.8 inxi: 3.0.37 
```


**Issue description:**
Hi,

In the following screenshot, you can see a Godot logo. Like many of us, I use it to create some prototype scene. It be use inside a `Skin.tscn` and add as a child of `DummyEnemy.tscn`. `DummyEnemy.tscn` is added into the level. It appear as expected in the editor preview.

![image](https://user-images.githubusercontent.com/1162446/85927667-e9d01980-b8a7-11ea-9d58-c3bc3619ede6.png)
![image](https://user-images.githubusercontent.com/1162446/85927699-15eb9a80-b8a8-11ea-826f-d4143ef65b7d.png)

I set the `Skin.tscn` position at 0,-32
But on runtime, the `Skin.tscn` is placed at (0,0)
![Peek 2020-06-27 19-01](https://user-images.githubusercontent.com/1162446/85927792-a88c3980-b8a8-11ea-982c-09cf63dd1828.gif)

**Steps to reproduce:**
I can't hardly know how to, since I use the same method for my `Player.tscn` and the problem didn't occur. Both use a an inherited custom scene that inherit from my main Skin.tscn.


**Minimal reproduction project:**
I try to create an unique project but the issue didn't occur. Here the current project with the problem. You just need to open TestRoom2.tscn.
[godot-2D-platformer-template.zip](https://github.com/godotengine/godot/files/4840956/godot-2D-platformer-template.zip)

Thanks!