Those financial numbers - assuming they are trading losses and not the "gone concern" losses - are truly shocking. By that, I mean that when an airline defaults under a lease, the lease contains a term that all remaining payments until the end of that lease agreement become due and payable. If you had 50 aircraft at $100k/month each, your lease rental outgoings this month would normally be $5m. If you ceased trading and each lease had 5 years left to run, the lessors would suddenly consider that you owed $300m and so all of a sudden, the amount owing when you've gone bust is several multiples of what you'd have paid out if you were still trading. If the £215m loss is before any of those penalty payments were claimed, that's unbelievably bad.
In terms of the aircraft, the situation is not as shocking as it sounds. Within a large fleet of aircraft, it is inevitable that things like engines, props and gear legs will be swapped around over the life of the many aircraft in the fleet. Aircraft A might be delivered with engine serial numbers 1 and 2 installed; aircraft B has engine serial numbers 3 and 4, and the airline has a spare engine number 5. By the end of two years, you'd probably find that aircraft A has engines 2 and 5 fitted, aircraft B has 1 and 4 and engine 3 is sitting as the spare. However, each engine technically "belongs" to the aircraft with which it was delivered.
When working towards your handback dates, you'd routinely try to swap engines and major components within the fleet so that each aircraft arrives at its end-of-lease date with the right engines, props etc installed. At least, that is what you should be doing. In the case of Flybe where everything came to a sudden stop, it means that the components would not be attached to the right aircraft. If just one leasing company then insists on having Aircraft A redelivered with engines 1 and 2, and they won't accept engines 2 and 5 as fitted, you're into a major fleet-wide exercise of having to swap all of the out-of-place bits back. That's what has been going on here. It does not automatically mean that the aircraft were in a poor condition - I'm sure that they were not, but it just means that they were not in line with the required conditions at the end of the lease - due to the abrupt termination of it.
There were some regulatory findings and issues, so I've been told by people very close to it. To the best of my knowledge, those aren't the same as the issues being referred to here which are really about the leasing companies exercising their contractual rights to the property that they own - and perhaps one or two being precious in the process about what they will and won't accept.