Hi Mark,
Yes I can see how it makes life difficult and there would be some room for confusion between early war variants of the same aircraft and later variants. I guess this would have to be be tackled by:
a.  Having effectively two different aircraft with similar look/ name but with different move charts.
b.  Scenarios that determine which version of the aircraft is used dependant on date. This might mean re-working existing scenarios which I can see would be a huge amount of work. 
Was just an idea. Guess I'll have to resort to CE for my early war fix! 
 Regards,
Neil