Before I make things worse (registered second base game code - game won't start)

I think it was the fact that the new game was Steam. Store content is very picky on "recognizing" if it's the same owner. Digital download games versus discs and Origin versus Steam - they are in slightly different locations or have slightly different codes. So, the powers that be (DRM) decide that you might not be the owner of the store content after all. Last check was an Origin Digital Download or disc. This check was a Steam version. The two don't match, so the game won't load your store content. I'm glad you got all your stuff reinstalled so quickly!