now that she has freedom, she won’t lay in the nest box, but chose the tiniest flowerpot in my greenhouse (that’s a whole nother story) to lay her eggs

Because they have survived on their own for at least 2 months, they are perfectly capable of evading predators, as well as their original owner and you. You will not be improving their safety by locking them in a little coop.for reasons i do not know, they picked me to live with.
they have been in my backyard for 2 months. they are here all day and have been sleeping in a different neighbor’s trees at night.
the neighbor who they belonged to originally, has tried to catch them for ages and could not. but they befriended me and follow me around so he said i could keep them.
she had no choice if she was locked in.we got a coop with a little run (we will make a bigger run very soon) and i kept them in there for about 6 days. louise seemed to be taking to it the best. she lays an egg almost every day in the nest box and goes right up at 6:30pm.
how would you like being thrown in jail out of the blue?thelma had a harder time getting adjusted and was a bit panicked at first.
they are safer when free, they can run and hide then. See all the posts on BYC about massacres in coops when predators get in. Or parasite infestations that make their lives a misery.what is the best thing to do? i am sure she will be back tomorrow. neither of them will let me handle them, but they will eat out of my hand. and i can get her into the run with bribes. i just want them to be safe.
No. If you leave the door to the run open, and they trust you not to imprison them again, they may choose to come and roost in there, and you could shut the door to the coop for protection overnight. Then let them out again to range freely in the morning light.should i lock them in again? for longer?
Just leave the run door openshould i just get them in the run earlier since they will go up once they are in?
they have good taste.they seem to prefer grass and bugs
Mine choose to sleep in coops (with occasional exceptions) and roam free dawn till dusk. Most lay in the coop nest boxes but some prefer flower pots/planters as one of yours does. One even incubated a chick in there, and raised it outwith a coop for 6 weeks. The predators here are the same as you face plus adders. They are safer outside and much happier and healthier than they would be if locked up, standing in their own waste, breathing ammonia-filled air, nothing to do, no forage, no exercise, no freedom. They came to you because they wanted to. They will stay if you are nice to them. Love is an open hand not a closed fist.