It's completely your choice. Do you want to breed them? Do they have interest in have a second clutch? Then leave the box and let them try again. If you don't want to or the have had more than 2 clutches this year, it's best to remove the box and reduce their hormones with giving them longer nights which mimic winter time.
Don't throw out the dark one yet because something different is going on with that one. It's either DIS or fertile and close to hatch time. It's not always easy for an inexperienced person to tell the difference between a dead egg and one that's ready to hatch. The embryo fills up most of the egg so light doesn't travel through it easily, and it looks dark when you candle it.
^ I was gonna say, keep the dark one for a while longer. All of my fertile eggs are almost completely dark (minus the air thing) around the due hatch date because the chick is so big and ready to come out.
If you have a spare few minutes, take the dark egg into a super dark room (or just do it at night) and shine a light in there and just watch it for a bit. Generally before my eggs are ready to hatch, I can see the baby moving around inside it.
If the parents have stopped sitting on the egg there's a risk that it will chill and die without hatching. Or it may be dead already. But on the other hand, it's normal for the parents to let the egg cool down somewhat as hatch time approaches. It helps with hatching somehow but I don't remember why.
Infertile eggs don't normally turn dark. But if an infertile egg got cracked or damaged it's possible that some bacteria got inside and that's why the color changed. So basically anything could be going on here. But the best plan is to leave the eggs alone for now and see what happens with the dark egg.