As you may or may not know, BA Connect and Flybe have recently merged. Flybe were being taxed on their Flight Duty Pay,whereas BA Connect were not. The reasons the enquiries were being made with HMRC were so that Flybe could adopt the tax free Flight Duty Pay that BA Connect had. However, it is these enquiries which have raised the issue of tax payable of Flight Duty Pay, and the letters stated that it would apply to all airlines in the UK,and not just Flybe.
I remember one of the letters mentioning something to do with the company making a profit, i'll have to look at it and reread it.