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The rules (p17) state that the German player has the option of not "assigning" a mission to a flight. How are you playing this?
Presumably a non-assigned Mission card is returned to the deck as the pending pile is limited to 3 cards.
We just put it back in the pending pile/hand. The rule doesn't state that it's limited to 3 cards.
(In our Scenario 2 game last night I wound up not assigning missions to Luftflotte 5 (the Norwegian one) in both Turn 3 and Turn 4 - they were down to just one squadron card by the end of Turn 2).