LHN: You are right. I can' answer for Mr. Boeing or other companies, but we deal with flap retraction on our N-1 (to use the current parlance) missed approaches in exactly the same way as we would with all engines operating. We retract our flaps at Missed Approach Altitude.
Depending on the fleet and where the go-around starts, we have two methods of tracking where we have a non-standard N-1 take-off path. Our Jet jockies follow the Standard Missed Approach but the Turbrop guys take a different route. If they go-around below DA, they follow the Non-Std N-1 Take-off path.
But as ever, when things are looking marginal, Airmanship and SCD come into play.
PM