The Unity-Technologies Github is full of interesting bits of branching tech. The "de-lighting" is one such tool that can be found within the organization's repositories and does exactly what it sounds like it would do; de-lights photo-realistic 3D assets! De-lighting tools are useful while you are working in 3d space if you're looking to achieve level of realism.
Certain amount of retopo is involved in any type of photogrammetry
Correctly tweaking and/or "parameterizing"..should fix discolorization?