Skyscanner is just a comparison site that directs you to an agent. As far as Omega Flight Store is concerned, I've done some searching on them and their reputation isn't exactly brilliant, sounds like they're a cheap bucket shop agent.
As others have said, did he book by credit card?
Have you got a flight booking reference?
Get him to phone Etihad and confirm the booking


Hopefully everything will be ok, and there's nothing to worry about