In upper airspace aircraft have to fly according to filed flight plans
but if traffic and airspace permits shortcuts may happen, or the aircraft are provided with radar vectoring in case of conflicting traffic, active military areas, adverse weather conditions, etc.
Under those circumstances, I believe that the safest attitude would have been to follow the filed flight plan
with the pre-established altitudes.
The company said that pilots who register online and opt-in for ACAS via the Pilot Web Portal will receive alerts of new adverse conditions specific to their filed flight plans
via text, email and Iridium satellite devices.
SASS collects data automatically to calculate ETAs, from filed flight plans
and from a trajectory predictor, which regularly 'considers', for example, aircraft performance and regularly updated wind and radar data along the filed routes.
Both pilots had properly filed flight plans
and were in contact with Dublin Airport.