### Godot version

4.1.1 stable

### System information

Windows 10

### Issue description

this is the default size loaded on startup 1024 which seems fine but it actually have loaded the default [2048] and ignored the size in project settings
![image](https://github.com/godotengine/godot/assets/53877170/c8c71de7-468a-487f-8e6c-dba1ce0f8fa5)

changing it now to any size will break it 
[2048]
![image](https://github.com/godotengine/godot/assets/53877170/3082ff09-b7d7-41f7-8fbb-813074a54135)

[512]
![image](https://github.com/godotengine/godot/assets/53877170/5ea4620f-52b5-4d0e-a5f5-747e777cd59d)


### Steps to reproduce

change 2d shadow atlas size in project settings while using compatibility renderer. 

### Minimal reproduction project

_
state.canvas_instance_batches.clear();
		return;
	}
	
	glBindBuffer(GL_ARRAY_BUFFER, state.canvas_instance_data_buffers[state.current_data_buffer_index].instance_buffers[state.current_instance_buffer_index]);
#ifdef WEB_ENABLED
	glBufferSubData(GL_ARRAY_BUFFER, state.last_item_index * sizeof(InstanceData), sizeof(InstanceData) * index, state.instance_data_array);
#else
	
	void *buffer = glMapBufferRange(GL_ARRAY_BUFFER, state.last_item_index * sizeof(InstanceData), index * sizeof(InstanceData), GL_MAP_WRITE_BIT | GL_MAP_UNSYNCHRONIZED_BIT);
	memcpy(buffer, state.instance_data_array, index * sizeof(InstanceData));
	glUnmapBuffer(GL_ARRAY_BUFFER);
#endif
	glDisable(GL_SCISSOR_TEST);
	current_clip = nullptr;
	GLES3::CanvasShaderData::BlendMode last_blend_mode = GLES3::CanvasShaderData::BLEND_MODE_MIX;
	Color last_blend_color;
	state.current_tex = RID();
	for (uint32_t i = 0; i <= state.current_batch_index; i++) {
		
		if (current_clip != state.canvas_instance_batches[i].clip) {
			current_clip = state.canvas_instance_batches[i].clip;
			if (current_clip) {
				glEnable(GL_SCISSOR_TEST);
				glScissor(current_clip->final_clip_rect.position.x, current_clip->final_clip_rect.position.y, current_clip->final_clip_rect.size.x, current_clip->final_clip_rect.size.y);
			} else {
				glDisable(GL_SCISSOR_TEST);
			}
		}
		GLES3::CanvasMaterialData *material_data = state.canvas_instance_batches[i].material_data;