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I'm familiar with BEYs SMS system, and in fact if you turn up any sooner it's unlikely there would be anyone at the check-in gate. BEY has also centralised some of their security check operations recently, and an FTer who described it suggested that at peak times this could cause problems. At other times then 3 hours would be overkill, if HBO 1 hour or a bit more would be OK.
Did they turn up 3 hours early ? And were they the only person that didn't make the flight? If so what was the reason why they were badly delayed? If there was only one passenger then that would explain the stance of the ground staff in BEY.
Normally a return Avios booking is only semi flexible, so you can't refund the return, but you can change the return date. It is often suggested in this forum to only book single tickets outside USA and Canada since this generally gives better flexibility. I'm guessing the problem here is going to be that because of the no-show the return ticket can't be restored, so another reason for booking singles, or at least ringing BAEC (where possible) when a no-show is going to happen.
If the traveller genuinely did all they can to get through the system there are some court cases which give protection under EC261 in this scenario (albeit at junior court level) but my first suggestion would be to have another go on getting the return ticket to be restored to minimise further loss.