I shouldn't have to explain this... it should be self explanatory.
"Sure the noise she made and her increased heart rate was her maternal instincts kicking in, but how did she know she should protect them?"
Because they're her chicks.
"It suggests that she could put herself in their position and realised that it would be unpleasant."
No it suggests she feels a need to protect her chicks.
"Which is empathy."
Nope, it's not it's maternal protection. An instinct that virtually every living thing on this planet exhibits.
"The reason it might not work if you APC another hen's chick is that she wouldn't have cause to react to it even if she could empathise with their situation."
What ? Did you think about that before you wrote it ?
Or it might not work because she doesn't feel any maternal instinct to protect another hens chicks. Irrelevant of any empathetic capability she might or might not posses.
"The maternal instinct is what determines the nature of the reaction, the empathic response is what determines the need for a reaction."
I'm sure that was where I started, when I stated that all this proved was that hens exhibit the maternal protection instinct towards their own chicks. There's no empathy required at all.