The update neither changes nor removes any of the substantive material from the original story (look carefully). It adds additional material, and fleshes some of the previous material out.
It seems like standard practice at newspapers to get a first take on a story and then flesh it out later. It's certainly standard practice at The New York Times, as even a casual look at NewsDiffs.org will show you: all sorts of pieces are effectively rewritten multiple times between their quick-take online version and the final print version. The Times never posts correction notices when that happens; they post them when they get something wrong.
Later
A thread running through this controversy is that the new NYT story is an "opinion piece". Let's analyze it, graf by graf. This list is numbered by graf; the summaries are my own (you could dispute them if you wanted).
1. Pao is a hero to many online for her gender equality fight, but was ousted by people online as well. This is mostly beyond dispute, except for the presumption that the Reddit mob actually did oust her, which all the principals in the story deny. That interpretation favors the Reddit mob.
2. Pao's resignation was abrupt and happened amidst a torrent of misogynist drama, renewing concerns about SV sexism. It's indisputable that her resignation was abrupt. It's indisputable that the story has generated concern about online sexism. Some people may not appreciate that concern, but that doesn't make its existence not a fact.
3. There is a debate about online invective, particularly around gender issues. Calls for Pao's ouster focused on her failed KPCB lawsuit. First point: indisputable (see: GamerGate). Second point: indisputable (see: petition for her ouster). Second point particularly interesting because the suit has no obvious connection with Reddit.
4. Pao's lawsuit revealed a culture that prized machismo. This is the closest the article comes to opening up a salient in the debate. I happen to agree that the trial proceedings and community response did that, but reasonable people could disagree. It would be hard to argue that the Times simply made this up, though.
5. Pao's popularity amongst Redditors was influenced by the lawsuit. Again: indisputable; the petition for her ouster leads off with it.
6: A direct quote from Reddit's chairman about Pao asserting that misogyny payed a role. Reported story is reported.
7: Pao's unpopularity generated a petition, and lots of ugly comments. Nobody disputes this.
8: A direct quote from Pao's resignation letter. Reported story is reported.
9: A direct quote from Pao, and background on Reddit. Reported story: still being reported!
10: A direct quote from Mitch Kapor on the demographics of Reddit. Still more reporting. Three quotes in this story so far, two from the story's principals, one from an extremely well-known person in the industry.
11: Direct quote from Kapor about gender issues on Reddit. Kapor is corroborating points raised earlier in the article.
12: Many subreddits went on strike over the firing of Victoria. Indisputable, and also the event that precipitated the story.
13: Pao posted an apology over her mismanagement of the site that was somewhat broad in scope. Indisputable fact, directly relevant to the core issue of the story.
14: Pao's ouster is a setback, after losing a lawsuit and turning down a lucrative settlement. Indisputable fact.
15: Kleiner's side of the story is that Pao was a bad investor. That is indeed their side of the story. The Times does not rebut it.
16: Pao owes a large amount of money, which the judge believes she's capable of paying. Still more facts.
17: Pao is unclear on how she's going to proceed with appeals. Still more facts.
18: If Pao succeeded in her appeal, the legal showdown between Pao and KPCB could recur. Factual, and relevant to the story: Pao's suit was, again, in the lede graf of the petition for her ouster, and it could happen again!
19: Huffman is the new Reddit CEO and part time at Hipmunk. Indisputable facts.
20: Huffman and Ohanian started Reddit. Indisputable facts.
21: Reddit is a private company with 50MM in funding. More undisputed facts.
22: Pao is remaining as an advisor, looking forward to getting more sleep.
I'll go ahead and say it: by no reasonable definition is this an "opinion piece".