Oh dear! You must wait for further advice from owners of captive birds. But your situation is truly unenviable. Sedation sounds like it'll literally be your option.
As Wild Emu Guy, my thoughts are:
when talking about emu aggression, the pivotal thing is whether they have room to run away. My joke is always about emus only being dangerous if you are trying to back them into a corner, to stuff them in a bag.
Also: I advise teaching your emus to recognise a sound associated with food -- it's not gonna help you this time, but maybe next. If your sillies ever need to be lured out of somewhere, you can sit outside, and tap the bottom of a tin dish (the sound mine know). They will come to the sound.
The point is: if you can get the chicks to go where you want, Dad will likely follow -- ??
But today? It'll be months before this parenting male is likely to become less protective. Any scheme involving chasing them/driving them/trapping them may induce the sort of panic that results in injuries.
If sedation, I guess it'd have to be rendering Dad outright unconscious; trussing him like a chicken (massively powerful legs!); carrying him holus bolus into a vehicle; going back and catching the chicks.
We look forward to hearing how you fare with this.
Supreme Emu
