My
experience has been that chickens will eat anything they can find and once they find something they like, they will scratch around for more. It's not just the seeds at risk but also the swales. Chickens will scratch the soil down hill and leave gaps, hills and holes all along the way. If there is mulch, they will move it. So what can be done? Luckily there are a few things you can do.
1. Divide the space into paddocks so that there is some time when the chickens can't access an area that has recently been seeded. If you're trying to establish a whole new system, then you may wish to create a sacrificial space to keep your birds on while you develop the rest of the
land. By adding lots of mulch,
compost, logs, leaves, kitchen scraps and other materials, you can keep the chickens busy in one location while the rest of the property is establishing.
2.
Feed them in the coop before you let them out to range. They will fill up early and be less inclined to gorge on your newly planted seeds. Of course once you let them out, they will scratch and do what chickens do. At least with a full crop, they might leave more seed for your swales. Provide them a compost pile to focus on and they may ignore the seed. My instinct tells me this might be futile though. Whatever they don't eat, they will scratch and uproot.
Electric netting is my favorite option to rotate them around in. You could also make a chicken mobile or a coop and run system. Any
fence that's not electrified probably should have a covering of shade cloth or netting to prevent them from flying over.
I don't let my chickens onto any swales because they just keep scratching the mounds apart and filling in the low parts with soil and mulch. Most of the time they are in a paddock shift system on pasture. During the winter, they free range. My dog is trained to keep animals out of gardens and swaled spaces so that's a huge help. Once the ground freezes, I don't mind the chickens being a little more loose with the rules. They can't move frozen earth.
In your shoes, I'd probably keep the chickens off the newly swaled and planted areas until they are well established and the cover crops have a decent
root system. Then introduce them slowly and keep an eye on them. You'll find the right balance eventually.
Good luck