Some confusion here. EU rules as embodied in the Third Package (1993) state that, for regulatory oversight purposes, the competent authority is the state in which the airline has its principal place of business. For FR, that shifted from Ireland to the UK some time ago, and the UK CAA would love to get their teeth into FR, but neither FR nor the Irish CAA want that to happen so for the time being at least the EU rule is not strictly being observed.
However the EU is currently pushing through a revision to the Third Package and one of the proposals is to substitute principal place of business with 'substantially established' or some such language. At that point FR will be free to relocate to Lithuania or wherever, as long as they pile in just enough of their business to convince the regulators that it is 'substantial'.