I think the ATR operation and the Embraer operation are two very different things that must be appraised separately.
The E195 operation was clearly a door opener to attract carriers with A320/737 equipment by demonstrating that carefully selected routes have potential from SEN for an airline with slightly larger aircraft, but a much better sales force than Stobart/Flybe. I don't think that Stobart ever planned to operate those routes longer term. It was either a miss with the route getting scrapped or a hit so that it could be offered on a silver platter to a larger airline. After all, airports earn most of their money with passengers in the terminal, not aircraft on the apron.
The ATR operation is different as the routes are mostly to tertiary airports with no/little air services to the UK. There is no apparent airline which could take over those routes after some warming up by Stobart as most of the routes can only be served, volume-wise, by regional aircraft and there are very few airlines left in that category. So I guess Stobart will keep those routes if the overall calculation shows that getting those passengers into the terminal makes sense for Stobart with regard to its SEN airport ownership even if the routes as such do not generate a profit for the airline. The problem is that there is little room to expand that operation as the number of potential destinations that are small enough and near enough for an ATR72 is somewhat limited.