Oh Dye, I'm so sorry this has happened. That's a really difficult problem.
I totally agree with Rick about excluding them being the only answer. As they make long tunnels underground, the only way to exclude them is to cover the floor with 1/2" weld mesh and then join this to a 50cm. weld mesh skirt round the bottom of the sides of the run. Ideally, all the mesh in the run sides should be 1/2" - what size is yours? If it's big enough for rats to get through, or for foxes to get their teeth into, predators will get in somehow. Alternatively, lay slabs over the coop area - but they will still tunnel under the slabs and up at the sides unless the slabs are secured to the sides of the coop with mesh.
Have you found where they actually did get in? Even if you remove food to a secure place overnight, they will be eating it during the day, and that's how and why they get in. When the food isn't available overnight, unfortunately they get a sleeping bantam.
If this isn't practical because your run is too big, maybe you could make a secure area under and around the coop, and make a mesh division which would close off this end at night?