Binary scenes don't save instanced scenes in them

[Summersay415]

Godot version

3.6.beta3

System information

Ubuntu Studio 23.04

Issue description

When saving binary scenes, references to instanced scenes are not saved. So, reopening saved scene causes loss of references to instanced scenes (only topmost node is saved, without reference). This bug is 3.x only, 3.5.2 don't have it.
Caused by: #62408

Steps to reproduce

1. Create scene.
2. Instance another scene inside.
3. Save first scene with .scn (binary) extension.
4. Reopen it. Reference to instanced scene is lost.

2023-08-19.21-46-16.mp4

Minimal reproduction project

N/A

[Calinou]

Can you reproduce this in 3.6.beta1 and 3.6.beta2?

[Summersay415]

Can you reproduce this in 3.6.beta1 and 3.6.beta2?

Yes. Attached video with confirmation.

[EzraT]

I can confirm this issue. Same thing happens to me on Fedora 38 in 3.6-beta3

[Calinou]

If you can compile the engine from source, you could look into bisecting the regression to greatly speed up troubleshooting.

Use these commands to start bisecting:

git bisect start

git bisect good 3.5.2-stable

# This is 3.6.beta1's commit hash.
git bisect bad 632a544c6e8f847d6796846d44f01231d1744958

[Summersay415]

I will try it in free time!

[akien-mga]

git bisect good 3.5.2-stable

I would advise starting from 3.5-stable instead, bisecting two diverging branches will add more steps unnecessarily.

[Summersay415]

Bisected:

2ceb93bbeff6f5c7b6eed4ea79aff5f0574f4f92 is the first bad commit
commit 2ceb93bbeff6f5c7b6eed4ea79aff5f0574f4f92
Author: Francois Belair <[email protected]>
Date:   Sat Jun 25 15:51:37 2022 -0400
    Fix custom res caching sub-res even if no-cache
    Fixes #59686, fixes #59752

PR link: #62408

Also I saw some output in builds where bug was:

ERROR: Resource file not found: res://Node2D.scn::1.
   at: _load (core/io/resource_loader.cpp:288)
WARNING: Couldn't load resource: res://Node2D.scn::1
   at: parse_variant (core/io/resource_format_binary.cpp:298)

[akien-mga]

CC @Razoric480 @KoBeWi

[Razoric480]

Can confirm that it is saved in the .scn file (if the saving happens in 3.x but the loading in 3.5-stable, the reference to the external TSCN is maintained.)

[akien-mga]

Fixed by #81026.