Above: Charlotte Braun, a supporting character from Charles Schulz' PEANUTS strip. She first appeared on November 30, 1954. Her final appearance was on February 1, 1955. She was never to be seen again.
Comic strip characters who suddenly disappear without reason is the topic of The Mysterious Disappearance of Four Comic Book Characters at the Neatorama blog.
strip characters from PEANUTS, CALVIN AND HOBBES, FOXTROT and GARFIELD.
A drawing by Schulz of Charlotte Braun getting "the ax" from a letter reprinted from the Letters of Note blog.
There must be some more examples.
For instance, the grandma character from the early BARNABY strips by Crockett Johnson. She was literally cut out of those strips when they were reprinted in the 1940s and again in the Dover 1960s editions -- until Del Rey's 1980s paperbacks and Fantagraphics current hardcover reprint books have returned her.
Is Castor Oyl still in POPEYE?
And what about entire episodes of characters' lives that are referred to and never seen. For instance:
The Noodle Incident - CALVIN AND HOBBES
Let me know if you can think up more.
Kinda related: Unseen TV Characters
-- Edited from a blog entry dated November 9, 2009.