Instrument change not saved

I have a score for 2 flutes. Second flute changes back and forth to piccolo. When I write out the Flute 2 part by itself and make piccolo changes, everything saves fine. But when I write out the combined score for 2 flutes and make the piccolo changes for the 2nd flute, the saved score loses the piccolo changes. The "to piccolo" text is still there, but the part jumps an octave and playback is flute instead of piccolo. If you look at the pdf of the combined score, you can see what it looked like before I saved the score. The .mscz file of the single excerpt retains the instrument changes, but the .mscz of the combined score does not.