[quote="oshfdk" pid='71544' dateline='1759869154']I've looked through the microphotograph samples uploaded by @proto57, this one seems to show great variation in the ink density. I'd love to hear your opinion about this one.[/quote]

Hey, you are not questioning my Superior Pareidolia, are you?   :wondering:

[attachment=11608]

First, note that this image (like many other micrographs from the report) is out of focus on the right side, over most of the r.

Second, for brevity, in what follows I will state as facts many things are only my opinion with various degrees of certainty. Thus,
please assume an "I think that" inserted before each statement. 

On that micrograph (as in the Beinecke 2014 scans) I see four very different ink types, Rt0-Rt3, with well-defined coverage areas and sharp transitions between them.  Rt0 are the original traces.  Rt1 is the first round of retracing, that was applied to almost the entire text of this page, as well as many pages in the whole book.  Presumably, the few parts that were not retraced by Rt1 were still legible enough at the time.  Rt2 and Rt3 are later rounds that retraced a few glyphs and words, or parts thereof.

Rounds Rt2 and/or Rt3 may have been cases of what I call "back-tracing", when a scribe goes back and retraces some stuff that he recently traced himself.  The back-traced glyphs then may come out darker only because the pen is more loaded with ink.  But retracing and back-tracing are distinct processes from variations of darkness along the [b]same[/b] trace, due to variations of pressure, ink flow, speed, etc.  The distinctions between Rt1, Rt2, and Rt3 cannot be explained by such variations.

Between Rt0 and Rt1 enough time passed for the Rt0 traces become so faint that the owner decided to commission a full restoration of the manuscript.  The intervals between Rt1, Rt2, and Rt3 are less certain, but at least one of them was long enough for the leftover Rt0 traces, and possibly the Rt1 traces themselves, had faded substantially.

Specifically:

(A1,A2,A3) Surviving original traces (Rt0): very faint, with fuzzy edges, low saturation (more like gray than brown).  Visible not only as extensions of the other stages (like on the left leg of the k and at the top of the left half of the o), but also by the side of those later traces (like in the "armpits" of the horizontal arm of the k, its right foot, the bottom of the o, and the start of the r plume).

The extreme fading of this ink is puzzling.  Could it have been an organic (plant) dye?  To bad that the lab did not analyze this faded ink and did not even comment on this striking difference.

(B1,B3) The global retracing round Rt1 included the o and the plume of the r.   The ink is light brown with only a few darker (but not black) spots, apparently where the ink pooled into cavities of the parchment.  Unlike the original Rt0 ink, the Rt1 traces have sharp borders.

The lower half of the left leg of the k and its right foot may be Rt1 too, but faded a bit more than the other Rt1 traces; or they may be original Rt0, that survived better than other Rt0 traces.  The Rt1 Retracer was very careful and mostly followed what was left of the original traces, but he surely made some mistakes.  One of them probably was at the top of the right half of the o (flagged X2), which should have been thinner, like the top of the left half.

(C1) The partial retracing Rt2 here shows only in the lower half of the right leg of the k. It is darker than Rt1 and mottled with darker (but still not black) spots.  It probably was used on other parts of the k, excluding the left leg; but the loop, for one, came out crooked (note Y1) and had to be retraced or backtraced again.

(D1,D3) Round Rt3 here included the horizontal arm, the loop, and the top of the right leg of the k, as well as the body (i stroke) of the r. Note the sharp transition (at X1) between the Rt3 and Rt2 parts of the leg.  The ink is darker than the Rt2 ink, and has lots of very dark spots.  The white glints show that these are neither solid pigment particles, nor places where the ink pooled into cavities of the vellum, but smooth rounded lumps that rise above the surface of the parchment and tend to collect along the borders of the ink trace.  It looks as if the ink was a mixture of a water-based liquid with an oil-based one, and one of these phases collected into the black droplets while the other spread out evenly to give the brown stain.

[quote]To me the match between the shape of the dark ink blobs and the faint ink strokes looks extremely hard to explain by retracing. The dark ink from the base of r seems to flow perfectly into the line of the flourish.[/quote]

You mean at the point X3? As I see it, the original trace (A3) was wider, and the dark ink flowed only over the top 1/3 of that trace, for a little bit.  It is not strange that the new ink speads over older traces. Those would have traces of binder, which is probably more wettable than blank parchment.

All the best, --jorge