He's still the best thing about "Wings."

From my understandin5b4g, he wanted to leave "Wings" as early as the fourth season but he stayed. So when the sixth season came to a close, he simply left. He had left the show and THEN was cast in the sitcom "Ned & Stacey." After the two-part season premiere, "Burnin' Down the House", Church came back to "Wings" to do his final episode and yes, that is his final episode. He didn't make any more guest spots, though I read (somewhere) that he was invited back for the finale but he declined. He was, however, in the audience for the taping of the last show.
Also, NBC aired some episodes out of order. "Death Becomes Him" was made after Lowell left but it aired before. That doesn't matter, i was just explaining that by the production he left in the third episode, whereas in broadcast order his last one was the fourth episode.

I believe he left to go & do Ned & Stacey.