Does the fact that any Thomas Cook passengers would have been flying back by one type of flight or another not invalidate your reasoning - whether it be charter or scheduled service? With the failure having been in September I would think that the vast majority of passengers who had already commenced their travel would, by the end of October, be home - assuming that those travelling for a month or more will have had to maketheir arrangements to return. At the end of the day it is, to me at least, the over all number of passengers that count.
November will be the first month when we will see whether those passengers who had been booked with Thomas Cook have managed to rebook their arrangements.
With regards to the domestic figures then yes, I believe that Flybe decision to cut flights, albeit towards the end of October, will have had a serious effect on the performance. Maybe we should revisit those numbers when the CAA get around to producing the October statistics (they have still not published September's data).