Scene Asset modification on runtime

I’m not sure if it’s what is happening, but I’m randomly missing refs in some scenes on my project.

If I load a scene as an asset (cc.AssetManager.Bundle.loadScene), run it through runSceneImmediate, and change, let’s say, a spriteFrame inside a cc.Sprite property, ref in this scene, should it change the scene asset itself?

Using CC 2.4.3

Can you provide a demo that reproduces the problem?