You’re in ProTools and ready to make a mixout so you highlight your regions and press command+D to duplicate — what the — your midi has shifted away from your audio. This happens if you’ve identified a beat and the tempo before/after that section is different. Rather than go put the midi region back into place by hand, just select the tempo ruler along with the regions you’re duplicating. This will make sure your tempo map gets copied as well. Here’s a quick video to demonstrate.