And here's my comment reconciling two DCAU comic book stories featuring Two-Face, Paul Dini's "Two-Timer" from 1995 and Bruce Timm's "Two of a Kind" from 1996:
I don't think there's anything incompatible in these stories.
The events of the BTAS episode "Second Chance" happen. Harvey goes back to Arkham. He makes progress, and they're planning to have his restorative surgery once again.
The Joker plays his mind games with Harvey in the
Batman and Robin Adventures comic book story "Two-Timer," Grace ends her relationship with Harvey, and Harvey goes back into Arkham. Harvey again makes progress, and as he's now a single man once again, he's free to begin a relationship with his plastic surgeon Dr. Marilyn Crane. (Even though a doctor getting romantic with someone she's treating is a really, REALLY bad idea).
Harvey has the surgery. He's released from Arkham, and the events of the
Batman Black and White story "Two of a Kind" occur. Harvey relapses -- Possibly even worse than before -- and he's now in the condition we see him in for the revamp episodes. (My personal feeling is that after the additional damage he does to his face at the end of "Two of a Kind," Harvey's disfigurement is now beyond the ability of plastic surgery to repair, but that's just my personal headcanon and never stated on the show or in the comics.) And, when you factor in Two-Face's last BTAS episode, "Judgment Day," he's now developed an ADDITIONAL personality to contend with.
So yeah, despite incremental progress and isolated moments where it looks like he'll make a full physical and mental recovery, Harvey just gets worse and worse over time. One step forward, two steps back.