This is a slightly different issue from badges missing in the database. As Taz mentioned, if you look at the
Accomplishment Badge Listing, you'll find that the alternate names for the badges are in the database.
The problem here is the backend logic that determines whether or not the badge that was just reported for your character was legitimate. Since none of the trackers have ever needed to track and report changes in alignment up to this point, the backend logic very simply assumes that if you are a Blaster/Controller/Defender/Scrapper/Peacebringer/Tanker/Warshade you are obviously a Hero. And Heroes reporting a badge with a Villain name (i.e. Positron's Betrayer) don't make sense to its logic.
On the other hand, the backend logic automatically assumes that a Arachnos Soldier/Arachnos Widow/Brute/Corruptor/Dominator/Mastermind/Stalker is obviously a Villain. And Villains reporting a badge with a Hero name (i.e. Positron's Ally) don't make sense to its logic.
Any AT that is traditionally a Villain AT reporting Positron's Betrayer will verify with no issues. Any AT that is traditionally a Hero AT reporting Positron's Ally will verify with no issues. Until we can get the backend logic updated, there are going to be issues with ATs that are not sporting their traditional alignments verifying badges with names that change along with alignment.
This is also going to require tracking alignment. And that's going to take some updates to tracking programs. (Though, if all goes well, other changes we're looking at in that area should make the whole alignment point moot.)
Updating the database was the easy part. There's still plenty of work to be done.