how old is your son?
the qantas site makes it clear that unaccompanied minors travelling on jetstar OR partner airline flights will be subject to the unaccompanied minor policies of the carrying airline. qantas advises you contact the other airline before booking.
emirates offer an unaccompanied minor service provided the child (between 5-12 years) has paid the full adult fare.
is that the case here?
might be worth calling emirates to check if your child was on a full adult fare if they will accept responsibility, and then further, whether qantas will allow you to change the fare (free of charge I would hope) to a full adult fare. (or alternatively, to cancel the QF flight in it's entirety, and change to an EK fare)
if they are not willing, then you need to check if they will let your son fly at all. will they deny boarding?
if they will allow him to fly, it would then be your decision whether to allow your son to travel. my initial thought is that in the absence of negligence, the airline would not be responsible for your son. (so for example if your son got lost in Dubai airport and missed a connection, or had a nap and missed his flight, then no liability would accrue).