In the time between CGT and CIT I rerolled one of my characters (his number is 183726) on Freedom... He went from emp/dark to db/wp. I set up HS to update CIT the other day to test that out and it looks like that is working for this character except that the powersets are still listed as emp/dark. (oh, and I didn't change the origin and SG, so that isn't being tested in this).
On the one hand, I can see where you might figure that there's no reason to check for powerset changes normally. On the other hand, there have been times in the past when people have gotten incorrect powersets set. If people are supposed to delete their CIT entry to fix incorrect powersets, could you put a note to that effect near the powersets on the edit page? Or, maybe better yet, a button to clear the powersets might be nice to have there.
Anyway, let me know if this is working as intended or not. If it is WAI then I'll just delete the character in CIT and verify his badges again and whatnot. If it isn't, I'll leave things as is so I can test out a fix.
HeroStats stores the powersets in the Hero Configurations file, which is keyed by toon name. There is an option to Ignore Stored Powersets, which will force that toon to (suprisingly enough) ignore the stored powerset values. Or you can just delete the toon from the Hero Configurations, which will force HeroStats to look for the information again next time you play.