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

[ReneZ]

There is no question that the order of application was pigment, upper-margin stain, foliation. The green is offset from the damp of the stain, and the foliation wasn't damaged by the stain elsewhere. I haven't looked at f.42 under a scope, but I would be extremely surprised if the green was on top of the folio number.

This was looked at under a microscope during the Folger workshop. I had a look myself, and both the conservator and I could see that the paint was on top of the ink.

Now this is unexpected for several reasons, but on the other hand, it probably could not be otherwise. The paint lies on top of the parchment while the ink goes inside (mostly). So the question remains: even if the ink of the folio number were applied later than the paint (which is what one would really expect), would the result look like this, because the ink penetrated the parchment?

I cannot answer that, but it looks like something that can still be addressed and resolved using the right expertise. One specific detail is that this paint included small crystals which were obviously on top of everything else.

A second question is: would it be logical/expected for someone to write the folio number over an area where paint was applied? Would the number not have been written more to the left? This is subjective and may not be possible to resolve.