What ever is the reason for the theses costs, the SEN routes are Stobart's business with the commercial risk on their side. There were voices expressing concern when they decided offering these routes. What they did was wet leasing aircraft from Flybe to operate them under own risk under the Flybe label by also paying franchise fees (if they did not negotiate this away).
And then there were various changes in Stobart's strategy. The wanted to start operating the E95s much earlier but possibly failed to get the crews, so the flybe leases were extended. Now, that they have eventually acquired three E95s, they stop these routes. Not sure what are their plans for them now but they will have exactly the same problem that Flybe has with these airframes: How to make money with them?