I see this happen in at least two spots: 1. Seahorse race in Atlantis 2. Cancer room in Silent School when you become those little crab-like things It happens when you have Scrap of the Soul Cloak equipped. I am not certain if Extended Supercharge (chest mod) also comes into play. You start with a full SC bar... you are transformed for the necessary portion of the game play... when you transform back, your SC bar is no longer full. I expect my bar to have the same fill level when I am restored to me that I had when I started the mission. It may also be occurring on Titan Island when you do the mech suit mission, but I have not tested this.