The route is being transferred to FlyBE but the transatlantic is still bookable via Aerlingus through a codeshare, so it will have limited impact.
If the airline has operational issues, then they have to deal with them, every airline does them, you'll find many airlines have been cancelling flights at the moment due to pilot issues, I can think of a flag carrier in a similar situation … it's inconvenient but if the customer service is handled well then it will be fine and it sounds like they contacted the passenger in good time and found a solution