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The worst debugging problem I've had after replacing LQFP chips is some pins not making contact. You can almost always spot misalignment and solder bridges. But if you don't have exactly the same bump of old solder on the pads, some pins on the replacement chip can be held off the surface just enough to not join the solder pool. The pins might make contact only when cold, or only when you touch the chip.
I once spent a long day trying to figure what design or component problem caused my crystal to not oscillate unless I touched the chip. I was assuming that it was the added capacitive load from my fingers, when it was actually the pressure causing the pins to make contact with the board.
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