I'd work on getting them to come when called or signaled, using treats, while inside the run first and then letting them out from there. That way at least you'll have a way of recalling them if needed.
I'd also start with small increments of time, and keeping them close to the coop and run at first. You can use sticks or something similar to herd them.
I only let my birds out for a very limited period of time each afternoon but they're used to that so they don't fuss when it's time to go back, and they get a treat as soon as they return, so going back to the run is always something positive for them.
