Yeah, so that coop sounds tiny. So here's what I think happened. I think it got very inhospitable in the coop and run as you described. The chickens got to roost somewhere else for a bit and found out that it was MUCH better. Chickens like space and fresh air, and they got that. Now they don't want to go back because their old home, even when cleaned, is just not as good as sleeping outdoors.
4sqft per bird in the coop (Coop being the "house" for the chickens to sleep and lay in) is important for a small number of chickens like this so they each have room to maneuver their bodies in the mornings and at night. 4sqft (2x2') gives a chicken enough room to stretch their legs, flap their wings, scratch at the ground, turn in a circle, preen, jump on a roost, etc. without running into another bird. With only a few birds (2-3) the likelihood of both chickens preforming a space-occupying activity (such as listed above) at the same time is pretty high.
Now that's less important when you have 50 birds. The chances of every one of the 50 birds doing something that requires standing away form eachother at the same time is pretty low. So for more birds it's easier to fudge the numbers. In a group this small they really want that space.
So... The reason stores sell pre-fab coops like this varies but it comes down to money. This coop WOULD fit, say, 2-3 serama chickens. But they are this big:
Compare to a shamo who would not even fit into your coop:
http://www.asilclub.spruz.com/gfile...rot_beak_asil_by_mullapudi_narendranath_1.jpg
Or, alternatively, space concerns are considered arbitrary. Consider the industry standard egg battery cages:
https://p.globalsources.com/IMAGES/PDT/B1157555442/Automatic-Egg-Chicken-Layer-Battery-Cages.jpg
So they will always tell you how many chickens will fit into your coop based on too-tight quarters and then claim it's for small chickens or "industry standard" sizes (ie, 1.5sqft/bird). And they will gladly sell you tiny coops for tiny birds or insufficient space without saying "don't put full sized pet chickens into this" because money.
So, 4sqft indoors, 10sqft outdoors, minimum, per bird, until you have more than 6 chickens.
If you fix the mold issues in the run (the wired part of the coop), they may STILL not want to return because of how small the space is. And they will
probably live just fine if you force them to sleep in the coop now that the coop and run are clean. But they're making their preferences for sleeping location plenty clear, and there's probably a good number of things wrong with your coop/run that make it uncomfortable for them other than a few bugs.
So if you want them to WANT to go back into the coop, you should give them a space that's nicer than sleeping on your porch. If you want to force them to go back regardless of what they want, shut them into the coop and run for a few days like you're teaching them where to sleep all over again and they'll get the hang of it. But otherwise they've made it pretty clear that they think the grass is greener outside of their coop.
