Difficult one because understand reaction of being transferred from France to Lithuania. Not requesting a base sounds like a faux pas and something you would expect someone to do or check on. Especially when rest of colleagues would have been doing it. Did he not talk with any colleagues ?
Getting CEO asking you not to resign, while not explicity saying it because that brings its own issues, there appears to be a suggestion that he would be out of Kaunas within 3-4 months. No written guarantees but take somebody at their word.
It doesn't sound like Pilot was someone that Ryanair had any desire to lose but more like a series of screwups that could probably have worked out for him had he stayed.