IMO... You are going to need to stand your ground, and not cave in... and basically restart their training and establishing a routine for them about cooping up each night. They've already learned that they can choose to do as they please, and I'd say it's highly likely they will established their own routine of choosing to roost in the trees or on roof tops (where owls will most likely get them) and once they start roosting where they want they will most likely refuse to return to the coop/run all together. So it's better to nip it in the bud now, than finding feather pile after feather pile and having to replenish your flock in a few months if you start free ranging them at this stage.
If the coop is of adequate size, and they have plenty of roosting space and you want them to roost safely in the coop each night... then I'd feed, water and give them treats only in the coop, and yes force (herd) them all to go in every night at approx the same time, and lock them in every night, with an extra yummie treat as a reward consistently, for several weeks. They can go out in the pen each day, but into the coop they need to go before dark. Sounds like you may have a rebellious flock... and food persuasion goes a long way with teaching them to cooperate. They may need to skip a meal or 2 to once again appreciate food and become a little more cooperative. May sound a little cruel, but not as cruel as being painfully pecked at, clawed at, chewed on, shredded or ripped apart by a predator.
If you decide it's too much hassle to start over, they may do fine with always roosting in the run depending on your predator load in your area, but I'd be extra diligent about getting them back into the run each night. One thing to keep in mind tho, is that predator season is coming up, they will have young to feed, and predators can and will reach thru the run's wire to get your birds, and if there's any possibility of a predator digging under, believe me, they will. It's in your birds' best interest that they learn it's a good thing to get locked up safe each night... unless you are ok with the probability of losing your birds one by one.