Godot version: 3.1 alpha 3
OS/device including version: Windows 10 64-bit
Issue description: Using "Make Scene Root" deletes other nodes from the scene.
Steps to reproduce:
Create any scene with one node. Instantiate it in some other scene. Create other random node in the first scene. Click "Make Scene Root". Everything looks good so far. Save the scene, switch to another scene, switch back to this scene and all other nodes but the root node are gone.
I found another similar bug. I had a Level1 scene inherited from generic Level scene. Level1 scene had instances of Player and HUD which I decided to move to Level scene instead. After doing so, Level1 scene showed Player and HUD twice, which was a bit confusing since I had no idea which one should I delete. It turns out that it considered both pairs of these nodes inherited from base Level.
Before:

After:

Duplicates disappeared after saving and switching to another tab.
I think it's similar visual glitch as I described in original post. And it makes me question if it's visual glitch in that case as well and it should indeed be a destructive operation.
@ondrowan Just to confirm: did the original issue (not the second post) happen in an inherited scene or in a normal scene?
Create any scene with one node. Create other random node. Click "Make Scene Root". Everything looks good so far. Save the scene, switch to another scene, switch back to this scene and all other nodes but the root node are gone.
I can't get this to reproduce, do you have more detailed instructions?
@bojidar-bg I tried it with normal scene.
@DualMatrix I just tried it on MacOS with both alpha 3 and alpha 4, and cannot reproduce it now as well. Unfortunatelly, I don't have access to a Windows computer (where I was able to reproduce it on several occasions) for another 2 weeks or so.
@DualMatrix I replicated it in alpha 4 in the end, but didn't realize there's one more thing to be done. Given scene has to be instantiated in some other scene. I've updated original post.
Ran into this bug today and lost some work. Should be high priority imho, this is scary...
Given scene has to be instantiated in some other scene.
Hmm that seems weird, wonder why that happens, I can't really come up with a reason why that would change the bevaviour, will take a look.
So I tested a bunch and I'm totally stuck as to what causes this, usually when a node dissapears from the tree it's because the owner wasn't set properly but I checked and that seemed to work fine in this case.
It almost must have to do with it being an instance, since it only happens when you open a scene that instances it afterwards.
Does anyone know of a property related to instancing that might not be transferred properly from the old to the new parent?
I added special checks so you can't use on instantiated scenes, should avoid trouble in the future. Let me know if you can still get it to break (I can't).
@reduz I've just tried nightly build and the bug I've described in OP doesn't seem to be fixed. Nodes are still lost when changing parent of scene that's instantiated in other scene.
There, now it forbids you to do it on inherited scenes too.
@reduz Sorry for late confirmation. The original scenario I've described is still happening though.
Reopening then.
Just ran into this myself with Godot 3.1 stable and Ubuntu 18.04, and was not able to undo with CTRL + Z. I'm very much a beginner with both Godot and open source contributing, but if there's anything I can help out with, let me know!
Just tested this on 3.1 windows 10 and the bug is still there. Here's a gif to show the problem:

I also discovered this issue myself, days ago.
But notice after you save the instanced scene, you switch to another scene (that have that scene instanced), back to instance scene, the nodes will be deleted. BUT, do not save the scene now, instead revert it or reopen it. The nodes will be back.
I'm having the same issue on 3.1.1 stable. This is hampering my work progress greatly. Please fix ASAP
Most helpful comment
I added special checks so you can't use on instantiated scenes, should avoid trouble in the future. Let me know if you can still get it to break (I can't).