I'm no plant doctor, but the fact that they aren't recovering makes me think the roots are too damaged to do their job. Keep the things moist and in the shade and hope for a miracle...
In the meantime, I'd get some seeds in the ground ASAP, and/or start looking for new plants.
The good thing about warm weather is that newly germinated seeds grow quite a bit faster than they did back in March. Of course you'll never catch up, but you may not be as far behind as you'd think. And with the growing season running 'till November, you'll have little trouble growing chilies this year.