CustomNode in VisualShader gets replaced with Null box

[eiszfuchs]

Godot version:
3.2.0-stable (until latest beta)

Issue description:
One of the custom visual shader nodes gets replaced with Null node, rendering the shader useless.
When I saved, the shader looked like this:

Next time I open the project, it looks like this:

Initially, I was trying to reproduce an issue I had with VisualShaders in the game I'm working on, where the shader (the one that's included in the reproduction project) would show properly in the game when started from the editor, but in the exported game, the shader would render completely black and the console showed an error some function (pnoise4d in this case) would not exist, and it indeed was missing from the shader code. The generated code in the visual shader editor however would generate the shader code just fine.

So I created a copy of my project, removed everything that was not related, and my shader would export just fine now, but now I'm having issues with the shader save and load properly. I don't know if I'm chasing ghosts here, so maybe you can shed some light.

Steps to reproduce:

1. Open the project provided
2. Observe the screen being black in editor and a Null box in the shader.

It should render like this:

(Please help, I'm going insane over this.)

Minimal reproduction project:
https://github.com/eiszfuchs/godot-vs-issue

[arkology]

CC @Chaosus
May be related: https://www.reddit.com/r/godot/comments/fqtfon/missing_custom_visualshadernodecustom_nodes_in/

[Chaosus]

Strange bug, I'm unable to reproduce it anymore to catch the sequence of action leads to it...

[eiszfuchs]

I haven't checked out the latest versions, since some collision-related bugs blocked me from working on my game any further until I made up my mind how to deal with them. The bug might have been fixed in the meantime (there were quite a few updates since 3.2.0).

I'll try to reproduce again as well to confirm.