Well I personally can't see it as being bad for Aberdeen. It can only strengthen the longevity of keeping LHR going and reinforcing links to MAN. It remains to be seen just how hub centric the new business will be and hopefully not at the expense of still linking the regions.
I suspect airport management in the likes of CWL and DSA that are Embraer bases, will perhaps have more to give them concern about than their peers in ABZ, should a rethink result in the most capacity being focused on feeding the hubs.
BTW the Flybe brand will disappear and will become Connect Airways. The article in the link below repeatedly states that improving connectivity to Heathrow and Manchester will be paramount.
Business Traveller - Flybe brand to disappear as Virgin Atlantic and Stobart Group agree takeover