Rats are opportunistic predators who will attack at any hour, and often even aggressive mothers won't defend against them. I had a very experienced reliable mother lose 9 chicks in one night, first to a phascogale, then to a rabid rat. Hilarious, I know. First the carnivorous possum goes under her and drags out and disembowels babies, leaving them for me to kill; we catch the possum, remove it; then about an hour later there's a screaming rat waddling around the cage in mortal rabid agony, occasionally dragging out a baby to dismember... But not kill... Again, my job. Relocated the possum, killed the rat.
Another rat, different occasion, in broad daylight, stole from straight under the mothers a few baby turkeys and one chicken baby. It stowed them alive in tunnels, after biting into the turkey babies' heads to cripple them, but didn't harm the chicken baby. They will happily get up to anything they want in broad daylight, and it's incredibly hard to rat-proof a cage. They will even wait for you to open a door for them.
Hens aren't like wild birds that might abandon a baby because you touched it. I've raised hundreds of chickens, and even had some terrible mothers who cripple babies, including one who ate their eyes and brains, but have never seen any chicken eat a baby chicken, which is bizarre because they eat mice, rats, snakes, etc. And even more bizarre because they've all had constant access to all babies I've ever hatched. By now, surely, some hen would have eaten a chick, if they were inclined.... But all my losses have always been acounted for. If you didn't see the hen do it how can you be 100% sure? However, if you are sure you're sure, then I guess you should cull or rehome the hen. It's up to you, but I don't personally keep any bird of either gender who I don't trust with chicks.
