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It looks like this.
This is a very protective Ruffles (mother) allowing Cillin (father) to imprint their chicks.
The rooster lowers his head to line his eye up with theirs and he stays in this position for a few seconds. He may even give the chick a gentle tap on the head once the imprinting is over.
As you can imagine, this sends some of the wannabe chicken momas into hysterics and high drama if they see it and the next thing you know there are a spat of kill the rooster posts.
Whether the rooster knows if they are his chicks or not is an interesting question. I believe they do but have no way of proving it.
There is as larger range of fathering behaviour as there is mothering behaviour.
Some roosters are baby gaga and others don't want much to do with them. Some will feed the chicks, others won't.
What I can write is I have never had a rooster harm any chicks be they his own, from his tribe, or from another tribe. I can't say it never happens but from my observations and from some of the more reliable members of BYC and of course the people I know who keep chickens, it's so rare it isn't worth worrying about.
Mothers and other hens however are a different story. I've had mother kill their chicks and attack another mothers chicks. Not often, but it happens.
Tribal conflict between mother hens who free range is pretty common ime. If one has plenty of room it's rarely an issue and the mothers either avoid each other or fight. Occasionally one gets an auntie hen in a tribe who thinks mum isn't looking after the chicks properly. I've had a couple of these. Mum may be tucking into some food and auntie will barge in and take the food and give it to the chicks.
If you see this then auntie is your next favourite broody hen and you should let her sit and hatch should she go broody.Don't interfere at all. We (humans) do not understand enough about chicken politics and chicken behaviour in general to make the right decisions.
Chicks are a dime a dozen in the chicken world. Most mothers don't seem to even notice if they lose a chick here and there. As long as they have one chick to mother they carry on with the job.
Roughly one third of the chicks I've known hatch didn't make it to adulthood.
Not a major issue for you I suspect but in places with a hight predator load it's the mothers and fathers you need to protect, not the chicks. This isn't a view that goes down well for those South of the Mason/Dixon line in the USA where the chicks life is viewed as most important by the wannabe mums.
The logic is however, a good broody mum will go broody again and have another go at hatching and rearing chicks. They tend to get better with practice. Lose a few chicks here and there is not pleasant but they can quickly be replaced. A good broody mum is worth her weight in gold as are good fathers
They call for me in the morning & come when I call them to bed in the evenings. Our shared interaction is a mutual agreement. I meddle in their societal arrangements as little as possible & debate over who gets to eat the silverbeet I planted.
The reality is neither animal nor humans life is ever going to be perfect but we can agree to share resources & muddle along together.
I will have to wait till she reappears, don my deerstalker and hopefully track her back to wherever she spent last night 
