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I have no idea if they are gone for good. One thing you can try is take the sim to CAS with the cheat active. Then randomize the traits. That will get rid of all the discovery traits. Then put the traits you had or want to have back on the sim. The discovery trait pop-ups should come back so you can add the traits again. They might be different than the ones you have as they seem to depend on what you have your sim doing when they pop up. This is the way I change traits on my sims, so I know it works, at least if you just want to change/get rid of one or more of the discovery traits. But it should also reset what you seem to have going on (hopefully). It's also the work around for a bug that was happening right after the discovery traits were introduced. I'm not sure if that bug has been fixed but what happened was when you changed a regular trait in CAS on a sim that had at least one discovery trait, it would corrupt the sim. So to avoid that, you have to get rid of the discovery traits first. Randomizing the traits does that and gives you a clean slate so you can reset the traits without corrupting the sim.
Hope this helps.
Edit: Since I last posted, I have been made aware of the thread for the bug I mentioned above. It is here: https://answers.ea.com/t5/Bug-Reports/OPEN-Retraining-potion-removes-additional-traits/m-p/12469945 . Since your issue is fairly close to what is in the thread, you might want to me too it.
That thread sounds extremely close to what I'm experiencing. I don't know if anyone at EA will fix it but, In the meantime, I may backup my save file and give your method a shot. Hopefully, like you said it may work.
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