So I finally figured out what was going on with this... It turns out it wasn't 2D simming that was causing the training to be reset, but rather importing/editing historical players.
I was in the middle of setting up a custom league, and every time I edited and saved attributes, all of the training boxes would get cleared for the player I just saved.
So now that I know the cause, (if I happen to edit any attributes in the future), I can just just reactivate the training settings for the player/players in question.
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