I'm experimenting on my leatherworker to see whether I want to invest points for learning a Bow of the Dragon Hunters. It's a Bestial recipe. I have zero points in Primordial Leatherworking. To get the bow recipe, I'd have to put ten points into that, then learn the Bestial Primacy node (which also grants +5 skill, as noted in the screenshot).

I find the recipe in my Unlearned Recipes section, enter simulation mode, and click the Simulate Knowledge Distribution button. Note that Missing Skill shows 45.

Next, I add the ten points to Primordial Leatherworking and "learn" Bestial Primacy by adding one point to make it zero. This reduces missing skill to 30, which is correct.

Finally I unlearn Bestial Primacy by setting it to -1 again. This does not remove the five skill from this node, and Missing Skill still shows as 30.

If I then remove the ten points from Primordial Leatherworking, Missing Skill shows I need 40 points, not 45 as in the first image.

Yes, resetting does return everything to correct values.

does it work when you reset? I recently rebuild the spec data, might have missed setting a node to unlearned when its set to minus 1! thx for the detailed report

This was a tricky one :) but fixed with 8.9.0 (release soon)