Not sure if this is a CIT or Sentinel bug, so poking in both places.
I have a side-swapped mastermind, who was previously tracked. When I look at her page, aside from the fact she's still showing up as a villain, her supergroup is still showing up as her old vg, not her new sg. Even deleting the character didn't help, as it was just recreated with exactly the same sg as before by Sentinel.
Still showing as a Villain: Definitely a CIT issue. It's one we should have fixed in the near future, but at the moment CIT hasn't any clue that it should even look for any alignment coming from tracking programs and it automagically determines you are a Hero or Villain based on your Archetype (because that's just how things worked prior to I18.)
Now, the Supergroup, on the other hand, that's going to take some small amount of investigating to figure out.
Would you mind linking the character you're having the issue with so that we can use it for reference in debugging?
OK, so here's what's going on with the Supergroup:
At the moment, Sentinel isn't detecting (or attempting to detect) your Supergroup. Rather, it's getting that info (and personal titles) from the records that CIT already has.
So, we know what the issue is. That's half of it. Can't say for sure when the fix will be available.