When you say it had "shifted downward", are you talking about the Y=zero position? Is that set by home switches, or did you set it yourself in relation to the stock piece you typically use? If the home switches are sending you to a new machine zero an inch from where the old one was, look for a flag that's been displaced (that's the thing that sticks out and triggers the switch). If it's a floating zero that's changed, simply jog the head to the place you want it and re-zero the Y axis DRO there.