What's the evidence that the colors were added later?

[MarcoP]

I find it interesting that on You are not allowed to view links. Register or Login to view. there is a massive painting instruction that was obviously ignored. The most likely explanation to me seems that the painter simply forgot to paint it.

Another simple explanation is it's no painting instruction at all. 

Isn't an explanation something that tentatively explains what the characters are and their function? Sure, giving up on finding an explanation is "simpler" than any possible explanation itself, but it’s not very enlightening in my opinion.

Alain Touwaide and Rene Zandbergen may be wrong about the color annotations, but it's a clear, well documented hypothesis, with excellent late-medieval parallels and supported by two very knowledgeable researchers.