Sounds like a very traumatic day for everyone. So sorry about your losses. I hope the new babies and mama are doing well today. You may have already considered this, but is there a way you could put up a mini run around the dog house you set up for them so that they are confined to that area and safe from predators? Just a temporary set up until the babies are stronger like a couple weeks. JMHO but I think separating the babies from her would be very stressful for both mom and babies at this point. Although I understand you feel they would be safest indoors, I'm sure you would rather see your hen raise her babies as long as you can keep them in a safe area. My suggestion is if you can get a pen set up, get those silkie eggs in an incubator as soon as you can get one. with the 3 babies there for her to care for, it should snap her out of setting. Hope you get everything sorted out!