It was always said that TUPE didn't apply in an insolvency situation and to be fair, I suspect Loganair probably had all of the advice in the world and arguments as to why it didn't apply, but lost that fight nevertheless. You have a lot of similarities between the two cases and the only indisputable difference I can see is the passage of time between Flybe 1 and Flybe 2. That might make enough of a difference all on its own versus the Logan/bmi case about whether there's a case that could be brought here and whether it may fail or succeed.
And when it comes to BALPA, there could be two reasons why they may go for it. First would be to support members who are either not in a job or in a job which pays significantly less than they had at Flybe 1. Second could be to support members who have got job offers at Flybe 2 but on significantly inferior T&Cs to Flybe 1 (as is rumoured to be the case) although that certainly would be biting the hand that feeds, so less likely. Parallels with Loganair again by the looks of it.
In other words, I don't think any of us can be certain until or unless this is put to the test in a tribunal. Until that point, even a legal opinion is just that - an opinion. Will be interesting to see if this aspect of the debate dies quietly or is rumbling along in the background.