there are quite separate areas of concern. One is air services agreements (ASA), some of which the UK holds under the EU umbrella. I'm guessing that someone is beavering away on independent negotiations with states with no dedicated ASA with the UK. It's probably solvable in the time remaining.

Perhaps more troublesome are the various safety/security/licensing arrangements we have among EU states. I don't believe the EU will be bloody-minded about any of this, but the UK might be relying too heavily on goodwill in an area where good intentions aren't nearly enough. Where rules apply, the EU is as much a stickler about their correct implementation as is the UK. Usually.