Our take: the flock dynamics here are playing out exactly as you'd expect when you drop two fluffy newcomers into an established social order, and that's not a bad thing. Your Silkie hen's mild pecking and avoidance isn't a crisis, it's a polite "I see you, but give me space" that any chicken keeper should recognize. This isn't Feathered fashion or fowl play: are your chickens now your wardrobe, where style meets the coop; this is real fowl feelings, and your Silkie hen is making them known in the most mellow way possible. Meanwhile, Tony the roo attempting to sit on the chicks is a cluck-tastic moment of paternal confusion that tells us your crew has a good heart, even if the chicks aren't ready for a feathery hug.
We've all been there, watching that first introduction and wondering if we've broken the peace forever. But here's the egg-citing truth: your birds are doing the work for you. The fact that nothing has escalated beyond mild pecking is a huge green light. Your Silkie hen is setting a boundary, not declaring war. And honestly, that's more than we can say for some of the fowl imposters we've seen in Which of my feathered friends is secretly a fowl imposter, at least your hens are being upfront about their feelings. The chicks retreating from Tony isn't rejection; it's self-preservation from tiny brains that haven't figured out he means well yet. Give them a few days of supervised free-range time, and those little silkies will start to realize that big fluffy Tony is just a gentle giant who wants to warm them up.
Should you encourage them to roost with the others? Not yet, and here's the takeaway: don't rush the roost. Your current setup, cozy shed overnight, supervised daytime mingling, is textbook integration done right. Pushing them to share a roost before the Silkie hen is ready risks turning that mild pecking into something less playful. Instead, wait until you see the chicks confidently approaching the big hen without her fluffing up, or until the Silkie hen starts ignoring them entirely. That's your sign to try a shared night. Until then, keep doing what you're doing, and remember that Meet Adam's feathered ladies: Gertrude and Nikki steal his heart, sometimes the best love stories in the coop start with a little awkward avoidance before the cuddle puddle forms. Watch for the moment your Silkie hen lets those chicks eat near her without a sideways glance; that's the real egg-citing milestone.