Instanced scenes gets overwritten to null randomly on open scene tabs

### Tested versions

4.3.stable Mono

### System information

MacOS - M1 Pro - 4.3.stable - Mono (C#) - Vulkan (Forward+)

### Issue description

Everyday, my opened scene in the editor are randomly overwrited - all their exported properties - with null. All connected signals are removed. Thankfully I have Git to catch these, but this is very concerning as any opened level or prefabs become completely broken.

Here's some of my git diff so you can see what's hapenning:

Any workarounds or ideas why this might happen is welcome - I'm desperate.

### Steps to reproduce

Unfortunately, I have no idea how to reproduce it, I'm sorry.

This issue wasn’t happening a few weeks ago. The project got bigger, so it could be either a scale issue, or related to a tool script I added that instantiate scene along a Path3D. Aside from that, nothing has changed.

### Minimal reproduction project (MRP)

Sorry, I can't reproduce.

No source file, test, reproducible entry point, or minimal reproduction project is provided. Start by comparing the affected scene files with the reported Git diffs and investigate whether the tool script that instantiates scenes along a Path3D is involved; done means identifying a reliable trigger and preventing exported properties and connected signals from being overwritten.

Written by the indexing model from the issue text.