I wouldn't call that episode a reconciliation.
They brought Chef back, but they played him off as having been to a brainwashing cult, that turned men into pedophiles...
It was basically ripping Scientology, again, on the show, that i think caused Issac to leave it in the first place.
Chef died at the end of that episode
Hayes left the show after the episode "Trapped in the Closet" where they made fun of Tom Cruise, John Travolta, and Scientology.
The last episode that featured Chef was called "The Return of Chef," but it was made
after Hayes announced his departure from the show, and he didn't record any lines for it. Instead, all of Chef's lines are cannibalized from previous episodes, sometimes in an ironically obvious fashion.
In that episode, Chef was brainwashed by the Super Adventure Club, which was an analogy of the producers' belief that Scientology had effectively brainwashed Hayes. At the end of the episode, they tried to get the message across that they didn't blame Hayes for leaving the show, but rather they blamed Scientology.
I'd always hoped that Hayes would one day return to the show as Chef, as I think the producers probably would have been eager to welcome him back. Sadly, that won't be possible now.