writing differences that I noticed

[ololololo]

The black arrows indicate the "bolder" letters. This could be a retouching, or the author could have underlined them to make them more visible. The orange arrow shows an example of a letter being erased, with the top line of the p almost invisible.

To positively demonstrate retouching/retracing one needs to show obvious parts of underlying strokes, as clearly seen in my examples above. One may argue that these have faded away to nothing, but given a full page of all grades of fading it's hard to believe this, if this was retouching there should be very obvious traces of previous writing in many places.

The coincidence of bold (wider) strokes with darker ink is possible to explain with poorly mixed ink. Different fractions of ink may have different viscosity and flow differently, the same movement of the quill would produce wider strokes flooding the parchment a bit.

Overall, I'm not sure there is one single explanation for these features that would satisfy everybody. My main point is that retouching/retracing, while the first thing that comes to mind, doesn't explain the visible absence of previous writing. Especially considering we have multispectral images now for a few folios.

But it's most likely a problem with the ink. The authors had issues with it, and a notable example is Herbal B, which is too dull and "watery".