Before I started using F.lux there was an obvious taxing period around 1-2am where my eyes might have started to get blurry or headache would set in, assuming I had woken up and started working by ~8am. From there I would either go to bed or brute force the next few hours, despite being aware of the time in general. Now, I don't get that feeling until much later– either at 22hrs when the sun has come up and F.lux begins fading out, or a little later if I'm not paying attention until after the sun has come up and the screen's been blue for a while. (At that point, I either notice the sun through the trees or get a splitting headache).
To further describe where I work: shaded area, floor to ceiling books, no clock, no phones. I do graphic work during the day and by early evening I'm in the command line until whenever. I can usually get out during the day, but sometimes I just don't. I think the proper advice here would be to stop working at home while living in the city, but that's enough OT– I was simply pointing out my experience using F.lux!