That also seems to happen when trying to cheat away the skeleton curse from JA. It seems to make it permanent. From what I remember, you would have to cheat that curse back and let the sim finish the curse (phase) to make it go away.
Since you stated this was actually a trait though, I can't be sure it would work the same way so I'm going to tag @rosemow for her advice. Nevertheless, I would advise you copy your save folder somewhere else on your computer before trying anything in case something goes wrong. The Guru's are warning some cheats can mess up your game.
As you probably already know, for general troubleshooting, you might want to clear your caches, especially localthumbcache, as it keeps hold of and uses old info making some new changes not work correctly. You could also try repairing your game. Oh yeah, and moving your mods folder (if you have any mods/cc) to your desktop to test out this change to make sure none of them are causing this not to work.
If possible, you can also revert to a previous save before you cheated that phase away to restore your teen back. Just make sure the teen doesn't age up while in a phase. I too wish there was a way to permanently do away with some phases but I haven't seen a solution for that.
