Since Multiform characters are bought using Total Points, all you have to do is remove the required Disadvantage from the character sheet and place that point total with Experience. For example:
DF: Yellow (Concealable), 10 points, can be replaced with Experience, 10 points, once the character learns how to stop being yellow.
This should be done through role-playing and character development if the Multiform's point totals have not changed between the two version. So the Multiform character might still only have 350 points (and thus not affecting his total value), but only 140 of them are now from Disads. The other 10 come from "free" Experience that the GM has given the character due to character development.
Monolith, the Living Titan
"The HERO System is not designed to represent real life. The game is designed to represent heroic fiction as presented in comics, novels, television, and movies."
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