Update 5:33 p.m. The Times public editor Margaret Sullivan weighed in on the AIPAC issue and more or less came to the same conclusion The Atlantic Wire did. The story wasn't changed significantly enough to warrant a correction because the information still existed in some fashion elsewhere on the site: 

The Times does not provide an editor’s note for every revision, although it does append corrections if a version included a factual error. Given the number of changes — new reporting, different headlines, more complete editing, etc. — that may come along in the course of a single news cycle, an editor’s note discussing each one would become absurd. If the meaning changes, as I believe it did in the Iran article I mentioned above, that ought to be explained. If, during a single news cycle, an article changes significantly, as in the Romney example above, a new article and new URL should be assigned.

She also cleared up an conspiracy that AIPAC requested the reporting be removed. "None whatsoever," David Leonhardt, The Times' Washington bureau chief, said when asked if they heard from AIPAC. "AIPAC remains a newsworthy part of this story, and you’ll see more about that soon."

Original: Media sleuths spent their morning trying to solve the mystery of The New York Times' disappearing AIPAC passage — which quoted an unnamed Obama administration calling the pro-Israel group the "the 800-pound gorilla in the room" during White House Syria discussions — but they chased some bad leads and didn't see the answer staring them directly in the face. 

Late Monday evening, The New York Times posted a piece titled "Obama pushes for approval of Syria military strike," which in its original form featured these two paragraphs:

Administration officials said the influential American Israel Public Affairs Committee was already at work pressing for military action against the government of Assad, fearing that if Syria escapes American retribution for its use of chemical weapons, Iran might be emboldened in the future to attack Israel. In the House, the majority leader, Eric Cantor of Virginia, the only Jewish Republican in Congress, has long worked to challenge Democrats’ traditional base among Jews.

One administration official, who, like others, declined to be identified discussing White House strategy, called AIPAC “the 800-pound gorilla in the room,” and said its allies in Congress had to be saying, “If the White House is not capable of enforcing this red line” against the catastrophic use of chemical weapons, “we’re in trouble.”

The piece appeared in Tuesday's edition, but around 5 a.m. ET on Tuesday morning, The Atlantic and Bloomberg View's Jeffrey Goldberg noticed something: 

Something seemed amiss in the land of the Grey Lady. But thanks to the wonderful power of the Internet, where nothing ever disappears from the record, even if The Times had wanted it to disappear, the quote didn't disappear completely. Some people noticed the passage still lived in the version that ran in the Boston Globe (which until last month was owned by The Times) syndicated version of the story, though. 

People began wondering where and why this newsworthy passage about an important, influential lobbying group's work on Capitol Hill to whip votes for the President's plan to strike Syria had gone, and the Times remained silent about the whole thing through most of the morning. There was no update or correction amended to the story online, which had been almost entirely rewritten. The Times' passage about "the 800 pound gorilla in the room" became its own 800 pound gorilla in the room as Times watchdogs began sniffing for a possible explanation. Times' political reporter Michael Barbaro got into a spat with Huffington Post media reporter Michael Calderone over the missing quotes: 

Blogger MJ Rosenberg noticed the missing passage, too, and offered this theory: "Obviously the White House and/or AIPAC did not want to be caught saying that the reason we are attacking Syria is to show AIPAC, the “800 pound gorilla,” that we are serious about the war the lobby really craves: Iran." Goldberg offered his own perspective, and confirmed the AIPAC's lobbying, in an interview with Politico's Dylan Byers. "I don't know what's going on, but it's very strange. It doesn't make sense that it was cut for space in the print edition, because the AIPAC passage was quite newsworthy. Plus, there's obviously no space issue on the Web. It seems plausible that someone from AIPAC, or the White House, complained about the accuracy of the passage," he told Byers. 

But the whole thing is actually a misunderstanding. In fact, the quote still lives on the Times website, but in a different article. It appears the media hounds never did a full search of the Times website to find it. After a morning of silence, Times spokesperson Eileen Murphy offered this explanation in an emailed statement to Byers just after lunchtime. It was removed to prevent redundancies: 

We regularly edit web stories for the print paper. This particular change was made to avoid repeating the same thought which ran in a page one story on Monday. That article entitled, "President Seeks to Rally Support for Syria Strike" included the following:

"One administration official, who, like others, declined to be identified discussing White House strategy, called the American Israel Political Affairs Committee "the 800-pound gorilla in the room," and said its allies in Congress had to be saying, 'If the White House is not capable of enforcing this red line' -- against catastrophic use of chemical weapons -- 'we're in trouble.'"

See, the piece for Tuesday's paper was written by Jackie Calmes, Michael Gordon, and Eric Schmitt. But, for Monday's front page — that is on Labor Day, when most of the Times watchdogs were probably enjoying the holiday — a piece written by Jackie Calmes and Michael R. Gordon had the exact same quote. And there it is, published online on September 1, the very article referenced by the Times spokesperson, sitting in plain sight on the Times website with the gorilla quote included. There's even a correction amended to the bottom of the piece: 

An earlier version of this article misstated part of the name of the pro-Israel lobbying group one Obama administration official referred to as “the 800-pound gorilla in the room.” It is the American Israel Public — not Political — Affairs Committee.

The scrutiny media observers give the Times is both warranted and deserved, but this is a case where things may have gotten a little out of hand. We're all coming off a long weekend, but maybe some people needed two coffees this morning.