The bill for the compensation for passengers left stranded and forced to re-book could reach €20million.
Pilots in 33 airports across Europe were roundly rejecting the cash offer, instead demanding improved working conditions in their contracts to take on extra work before October 31.
Ryanair's chief executive Michael O'Leary said that people whose flights are canceled will be transferred either to another flight on the same day or to a new schedule a day before or after their original date of departure.More news: Hurricane season isn't over, as Maria is about to follow's Irma's path
The letter said: "The pilot market is changing, and Ryanair will need to change the ways which the pilots and management work together to ensure a stable and common future for everyone". In the past year, Ryanair has lost 140 pilots to rival operator Norwegian Air.
"We have some goodies to discuss with pilots, but if pilots misbehave, that would be the end of the discussion of the goodies".
The French broker's analysts said: "We consider the ruling of the ECJ a risk to Ryanair's cost base going forward". "It seems clear that Ryanair has failed to plan properly for the implementation of the regulations".
The airline earlier this week announced that it plans to scrap 2,100 flights over the next six weeks, due to a crew shortfall which the company has described as a temporary problem caused by "messing up" an administrative change to the calendar.More news: Emmys 2017 red carpet
James Daley, director at Fairer Finance, another consumer group, said: "Ryanair has made this mistake and it needs to be gong out of its way to help customers claim what they are rightfully owed".
It's also recruited 125 new pilots to prevent further flights being cancelled.
They are said to be looking for permanent local contracts for all employees.
Separately, some Ryanair pilots have spoken to the BBC about a "toxic" atmosphere and how they felt "undervalued".More news: Iraq's Kurdish parliament backs September 25 independence referendum
The company's colourful chief executive Michael O'Leary announced the recruitment drive at Ryanair's AGM meeting, now taking place in Dublin.