Regression in 3d custom shaders not showing

[lawnjelly]

Godot version:
3.2 current branch 0a2a93b (13 oct 2020)
(It works in 3.2.3 stable, so has been introduced since then)

OS/device including version:
Linux Mint 18.3
GLES2 and GLES3

Issue description:
Sometime in the last 2 or 3 weeks a regression seems to have come in which is affecting custom shaders. I had been working on 2d so not noticed this. When I attempted to load an old 3d project the other day none of the textures were showing, but when I went back to a previous build they did show. I didn't test it thoroughly.

Today I opened some more 3d projects with custom shaders and again they are either black or showing as plain color, as if the custom shader is not working.

Steps to reproduce:
To test this I:

1. created a new project
2. added a MeshInstance
3. made it a box
4. Added a shader material
5. Wrote a basic unshaded shader
6. Assigned a texture

It shows correctly. However, after saving and closing the scene and reloading the project, the custom shader is no longer working. This even happens within the same project. When I created another box in an identical fashion and repeated the steps, the texture shows on the new box but not the old. I suspect after saving it will not show on either:

I've not pinned down what is causing this yet, I think it is a new regression so should be easy to bisect.

Minimal reproduction project:
Unshaded_regression.zip

[akien-mga]

No issue in 4040cd3 but I can reproduce in 0a2a93b, so the most likely culprit is #40313 (@pouleyKetchoupp).

[lawnjelly]

Yes I can confirm it appears for me in #40313.

I'll have a look through the PR and see if I can work out what is causing it.

[akien-mga]

Duplicate of #42675.