### Godot version

4.1 beta 3

The same project works fine on 4.1 **beta 1 and beta 2.**

### System information

Tested on MacOS, Fedora and HTML5

### Issue description

I have a problem in version 4.1 beta 3 with a popup (popup panel). The first time it always displays correctly. Every subsequent time, I only see a black spot. 

[Nagranie ekranu z 2023-06-23 11-35-28.webm](https://github.com/godotengine/godot/assets/5132385/f7a7ad08-754c-4b4b-b594-b6880eff5f3d)

*The same if I show popup by methods like popup_centered.


### Steps to reproduce

I'm trying to reproduce it with a clean and minimal example, but unfortunately, without success. Maybe someone else has this issue or knows a way to reproduce it?

### Minimal reproduction project

I'm trying to create it.
if (texture_atlas.textures.has(p_texture)) {
		texture_atlas.dirty = true; 
	}
}
void TextureStorage::texture_atlas_remove_texture(RID p_texture) {
	if (texture_atlas.textures.has(p_texture)) {
		texture_atlas.textures.erase(p_texture);
		
	}
}
GLuint TextureStorage::texture_atlas_get_texture() const {
	return texture_atlas.texture;
}
void TextureStorage::update_texture_atlas() {
	CopyEffects *copy_effects = CopyEffects::get_singleton();
	ERR_FAIL_NULL(copy_effects);
	if (!texture_atlas.dirty) {
		return; 
	}
	texture_atlas.dirty = false;
	if (texture_atlas.texture != 0) {
		GLES3::Utilities::get_singleton()->texture_free_data(texture_atlas.texture);
		texture_atlas.texture = 0;
		glDeleteFramebuffers(1, &texture_atlas.framebuffer);
		texture_atlas.framebuffer = 0;
	}
	const int border = 2;
	if (texture_atlas.textures.size()) {
		
		Vector<TextureAtlas::SortItem> itemsv;