If they are a Flybe franchise based in the CI it makes sense that they would operate all the current Flybe routes to and from the CI.
Why would they sign up otherwise?
Like
Loganair, they no longer want the overheads of a whole booking and marketing structure and realise that in some cases, franchising means economies of scale and shared risk. When and if this goes through, expect some major headcount pruning where flybe will be taking on the booking platform and the online sales.
Blue Islands started out as highe(er) quality and self handling, and sadly and predictably found the maket won't really pay for that. Hence they need to do something to put their struggling business onto a more sound footing, and that's to get into bed with a bigger partner.
As seperate companies and the bigger partner, flybe won't be handing over any profitable routes to the Channel Islands to
anyone unless it has a larger synergy to the business.