If you only use scratch as an enticement to return to the run, they will almost always come when you shake the scratch can and call them. The only time they won't all come is if you have some where important to go, and you need to leave... 5 minutes ago, but you are left playing the, "I just put 2 in, but when I opened the door to do so, three more ran out." game. When they play that game, and they love that game... it's their favorite!!! It's helpful to have a plan B. Like: close the pop door, so that all of the confined birds are in the run, then open the coop door (assuming it has an access door that is NOT IN THE RUN) and toss some scratch in the coop. Eventually, you can keep shuffling confined birds into the run, and catching the stragglers in the run.
WARNING: Never use bread or any other easily carried treat to try to get your birds confined, b/c they will grab the treats and then spend all of their time trying to escape so no one else will get the coveted treat.