Bug?:

So the problem is that when you turn off directional light skybox and GI takes other directional light.

Project Steps:

Scene contains two directional lights: Box02_Y1 and Box02_Y2

1. Hide and unhide Box02_Y1. (Skybox and GI chooses Box02_Y2)
2. Hide and unhide Box02_Y2. (Skybox and GI chooses Box02_Y1)
3. So even tough ("nothing changed from step 2") lighting changed to Box02_Y1.

Workaround:

Set one directional light with higher intensity, its seems unity always chooses light that have higher intensity.

I'm pretty sure its not a 100% bug and by fixing it there could be introduced even more bad behaviors and performance issues.