Soo I've been playing Reborn for about a week straight, and I've just beat Aya (only took me two tries ) and freed Heather & friends from Sigmund. Before I battled Sigmund, I decided to ditch the Chingling I was training to get its happiness up for the Bulbasaur event. So I dilly dallied my way back to the Pokemon Center and was messing around with my team line up on the PC. I had my Heatmor selected in the computer's little hand, then accidentally pressed X, but when I re-opened the PC, my Heatmor was gone.
This is what I mean when I have a Pokemon selected (Glameow).
Then from here, if you press X, Glameow will completely disappear. Completely boggled me.
(Don't mind Raticate. Couldn't find a better HM slave. >.<)