A company at the end of its tether will not be scared by some penalty clauses in a contract. If a company needs to restructure, almost any contract it will have to touch has some sort of penalty clause in it or carries the risk of a liability for damages because of a breach of contract - be it leases, employment contracts or a contract with an airport. So what? Do you think CWL or DSA will sue Flybe with the obvious result that there still will not be flights afterwards and a then insolvent Flybe is unable to pay? By entering into a 10-year-contract, those airports took a gamble and they knew it.
But let's assume just for the sake of this discussion that Flybe is indeed forced to keep CWL and DSA, which four bases would you identify that are under threat of closure as per The Irish News? Without DSA and CWL (and apparently BHD), make your pick of four from these eight: EXT, SOU, MAN, BHX, EDI, GLA, ABZ and DUS.