I am not really sure what's going on here. I made a very simple test, and everything seems to work as expected. So here is what I did:
-created the 2 lights with white color and 50 intensity
-auto setup light mix
-render
-changed light one to cyan, intensity 2
-changed light two to magenta, intensity 0,5
-save light mix pass
-in viewport select light 1, set color to cyan, intensity to 100
-in viewport select light 2, set color to magenta, intensity to 25
-render
-save beauty pass
Are you sure that after "baking" the LightMix values into your scene lights, you did not save your LightMix pass instead of Beauty?
In such case you would end up with LightMix actually altering the already baked values.
-save beauty