I'm just taking a guess, but maybe the lighting is linked to the stability bar.
I don't think so. Once it's green, I can get it off green by continuing to do the same Liq > Scission SC, which should lower the stability.
We thought about that too, but I haven't enough spheres to properly test it just yet, but it does seem unlikely as doing actions that should lower the stability can cause the light to reset.
I also don't think the color has to do with the stability, it went back to blue when the stability didn't budge. There must be another step required to be done during the green phase, which i assume will lower it down to the next level.
Perhaps after the bottom level is complete, a notch appears in the transmutation meter, a special animation appears on the machine, and the light returns to the top?
At first I didn't think the light had anything to do with stability, but now that I'm playing around with it some more, I think there may actually be a connection.
Thinking back to what I did the first time to get the green light, I just did a series of long level one craftchains. So I recreated that, and I was able to get it to change to green again. Video:
https://www.youtube.com/watch?v=pLNewVUaG1c
You can see that after several level one chains, the light changes to green. I then exit out of the Focuser, and reenter. You can see the light stays green.
I then waited a few minutes and reentered the Focuser, now the light changed back to blue automatically. This could have been time based, or stability based. It's possible that the light only stays green for a certain amount of time. It's also possible that it had regained enough stability to no longer be in the 'green' zone.
So I went and repeated what I did, a longer skillchain. I was able to get it to change to green again, however this time it was earlier in the skillchain. I also started with less stability. I then created some higher level skillchains, which according to Mewk, should raise the stability. At which point, the light did change back from green to blue.
I then once again started on a longer chain of level one skillchains, in which the light once again did switch back to green. I kept going with the lower level skillchains, until one of them broke, causing the Focuser to explode. I lost 5 spirit, the stability returned to full, and the light changed back to blue.
Video:
https://www.youtube.com/watch?v=CAXFppSHUJM
Finally, I wanted to show that the light will change from green back to blue on it's own after some time. So I once again did a lengthy set of level one skillchains, forcing the light to change to green. I then stood around awhile, checking the Focuser every so often. Near the end of this video, you'll see that upon reentering, the light is reset. Again, not sure if this is due to time alone, or the fact that stability went up. Since the second video shows me turning the light green quicker than the first, with the only real difference the starting stability level, I am inclined to believe there is a least some connection between the light and the stability level.
Video (warning, a lot of standing around at the end. 13:50 is where I go in and it changes back to blue):
https://www.youtube.com/watch?v=ZUeN0Ey7r7k
Hoping that all of this testing helps us figure something out, or if the light really is just another way of showing stability level, but that doesn't seem completely right to me. Hoping some others might be able to help figure something else out.