AgainstTheMachine. I'm not a pilot but I have had various dealings (through my employer) with HMRC. You need to engage professional advice - legal or accountancy, possibly both - now. If HMRC suspect something amiss (however misguided that suspicion might be) they have very serious powers - some of the normal 'presumption of innocence' may not apply - these powers are very much stacked in their favour.
The recent Court cases in the UK have been about employment rights (holiday pay etc) rather than tax per se. But the "colour" of noise coming out of Mrs May's government is that she and Hammond are not relaxed about disguised employment in the way that Cameron/Osbourne were.
Your perception of 'fault' may be with others (be it Brookfield or Ryanair) but HMRC may not agree - they can come after you if you made certain declarations on previous tax returns - the IR35 provisions are very relevant here.
I repeat: engage professional help.