An update:
Award seats on the direct ANA flight I wanted became available, so I phoned up the Aegean call centre and explained the situation - that I'd like to cancel the award I had and re-book on to the direct flight (going to a different city in Japan, with a different airline). It wasn't a problem, in around 15mins I had a reservation on the new flight.
The process as (1) hold seats on the new reservation; (2) cancel the old reservation (expected to take 10-15 days for the taxes for the old reservation to be refunded back to my card, minus the 20EUR fee which is non-refundable); (3) provide payment for taxes on new reservation; (4) wait for reservation details to be emailed through). To confirm, the agent handled all of this in a single call and it was a painless process.
Great service from Aegean!