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Well, if you wait until after dark, they'll be in there, and usually you can get to the pop door to close it before they start coming out. If I'm out there at night when it's open, doing things and making noise, they will wake up and wander out, but it usually takes a few minutes because they're groggy. So if you go straight to the run, and close the pop door, you should be able to close them in easily before they come running out.
Also, don't ever give them treats after dark. It's not that they're Gremlins, lol, but they'll get used to associating it, so they'll be more apt to wander back out if they hear you come outside after dark. A lot of times I suspect mine don't wander out much because they know they won't be getting treats until the next day. By then I would have already given them treats before sundown.