Example: one takes a trait at faction creation that gives them x bonus classes, for example Fey > Order > Unwavering > Bonus Classes 2 (sub-classes only).
It is stated that faction traits can be dropped without any drawback (aside from obviously losing the trait). Since the classes have already been made by then, can one subsequently drop the trait without losing the classes? Alternatively, would it be able to 'buy off' the trait for the amount of progression points it would've cost to create classes created with the trait (to remove the 2 point per model cost to get an early headstart)?
No. If you lose the trait the classes would also go away.
You could though remake the class using progression points later on. This would be a separate process. So if you later build the classes you did with the trait, then there would be no issue.