Sometimes, a character will gain or lose powers. A mutant develops a secondary mutation, or be "cured" of his powers and take up costumed crime-fighting using only martial arts and acrobatic expertise. An inventor builds a revolutionary power source that radically alters his existing tech, or crash his battlesuit in a remote area and have nothing but the local hardware store as a source of parts for new gadgets. A wizard might lose the valuable Ankh of Argon, depriving him of much of his magic, only to find out it was a secret test of character that unlocked new arcane realms of power.
In all these cases, the player should simply update his character's power facts. Such changes happen with the GM's approval, and can happen in play, or during a milestone.
If the character changes the aspect that provides them narrative permission to use powers, they should update their power facts to reflect the new reality.