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As BFS101 has said BCA will pass on these costs to the rest of the airlines using the airport and to the passengers. BCA will not be paying for the new runway extension from their own bank account so to say. Hence someone else [insert other airlines + pax's] will be picking up the bill.
If BHD based their contract with FR on the back of a runway extension happening, then that was a bit silly on their behalf.
Flybe have been at BHD since 1993 so 3 years is not exactly a long time, but I will agree with you, FR could have thrown their toys out the pram long ago and left.