First off I've been really enjoying following this build.
I use Vallejo paints as well and I found the airbrush thinner to be a bit aggressive and had a tendency to soften the paint below even when well cured. I haven't used the Glaze Medium but I have used a mixe of Thinner Medium + 1 drop Water + 1 drop paint. Will sometimes substiture Airbrush Flow Improver for the water since it has a drying retarder in it and is not as agressive as the regular airbrush thinner.
Life has kept me away from the bench for the last couple of months and your quandry got me curious and was a good excuse to get back to the bench, so I set up some tests to see how easy/hard it would be to correct.
Hope you don't mind an illustrated guide of my own attempts.
I had a "scrap" model hanging around that I had primed with black and gave it a good coating of "medium sea grey".
I then used a black sharpie to make some additional lines that I would attempt to clean up a little.
I made up a batch of the regular thinned paint with water. This usually takes a few coats to get a good solid color but has the benefit of leaving near zero in the way of paint ridges.
I could already tell it was was lighter than the rest of the base color.
Sometimes the flat coat will even out the color but it didn't really do much in this case.
I then mixed up another batch of thinned paint. This time using the Flow Improver and added just a smidge of black to it to darken the paint to better match the underlying black primer. What's on the toothpick is what I added. I did that twice. This mix tends to be a little thicker as the Flow Improver has a slightly higher viscosity but still goes down nicely.
Painted that as crossbars for comparison
Looking pretty good.
Hit it with the flat coat and this time the issue was reversed. The second attempt came out too dark.
I think that with such a dark primer coat this is going to be an issue of too light or dark if try to fix with the base color. However, you may have more success if the cleanup is done with the other colors you applied on top of the basecoat.
Hope my little test was of some help.