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Yes, it will readapt, assuming this actually is the problem. I don't doubt that it is, but I'm not saying it "has" to be the problem, but the mixture adaptation certainly will come back into line by itself, there is no real reason it has to be reset after replacing this part.
You may find it neccesary to use different throttle inputs when the MAF sensor is replaced vs with the old one because the mixture is being affected. The throttle position values will affect transmission adaptation (short term), so possibly this is why the transmission may be felt to shift differently. This is the only reason I can think of for the replacement of the MAF sensor to affect shift quality. Otherwise the MAF sensor has no direct bearing on shift quality.
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