The sanctioning bodies do what they want.
Hasim Rahman refused to step aside for Povetkin-Huck, but Povetkin didn't get stripped for that Jr WBA strap. Martinez said he wasn't stepping aside for (recent Chavez Jr opponent), but he didn't get stripped either.
Saying that, Khan is probably going to be fighting for his two former titles, so I'm sure whether he gets the WBC title or not isn't that big a deal for him.
If the WBC does strip Garcia, I imagine Olusegun will become the interim champion, and face the winner of Soto-Matthyse for the full title. At least, that would be what happens in an ideal world.