It's a side effect of the way permanent affinity was accelerated for Neutrality. DIK and CHICK Affinities became permanent when you burned away the last of the opposing boxes. Logically, permanent Neutral Affinity would require burning away enough of both boxes that would could no longer get DIK or CHICK Affinity anymore.
But that would have required about 2 more episodes to finish, and DPC evidently wanted to lock in all Affinities at the end of Season 2. As a result, Neutral Affinity is locked in if you
fail to earn one of the other Affinities with the final Major Decision in Episode 8. This counterintuitively results in situations where you lose your Affinity by trying to reinforce it; technically, you had already locked in Neutral Affinity some time ago, but the game didn't tell you about it until now.
Sadly, the only way to fix this is to go back and reverse enough Major Decisions that you'll be able to burn through that last box by the end of Episode 8.