LTNman
It has become rather confusing but I'll try to clarify things as I understand them.
Yes, when the ANR and MST routes were dropped Stobart Air operating as Flybe became a one aircraft operation so the second aircraft could have reverted to Aer Lingus Regional livery and operated the DUB-SEN route.
If Stobart reintroduced DUB-SEN it would presumably be under the Aer Lingus Regional franchise which currently operates eight ATR-72s plus a couple of ATR-42s. As far as the tavelling public would be concerned they would be booking with and flying on Aer Lingus flights so no question of it being a one route airline.
As the DUB-SEN route would revert to being an Aer Lingus route I don't see any conflict with the Stobart/Flybe franchise as Flybe no longer operate to DUB from LON.
As far as saying "there must be a very good reason" why Stobart haven't done this, well you would think so wouldn't you but I cannot work out what that reason is. I think it's worth saying that whenever the subject of new routes for SEN comes up on social media or in the press the return of DUB always features strongly. I would just say that if a large number of aviation professionals find their decision surprising and there seems to be a strong public demand for the return of the route then that decision remains irrational to my way of thinking.