Updated, 10:54 a.m., to add new observations based on reader response.

Bernie Sanders supporters have been unhappy with The Times in recent months, but it looked as if they were beginning to have their moment in the sun on Monday morning.

An article by Jennifer Steinhauer, published online, carried the headline “Bernie Sanders Scored Victories for Years via Legislative Side Doors.” It described the way the Vermont senator had managed a significant number of legislative victories in Congress despite the political independence that might have hindered him.

The article stayed in essentially that form for several hours online – with some very minor tweaks — but in the late afternoon, Times editors made significant changes to its tone and content, turning it from almost glowing to somewhat disparaging. The later headline read: “Via Legislative Side Doors, Bernie Sanders Won Modest Victories.”

And these two paragraphs were added:

But in his presidential campaign Mr. Sanders is trying to scale up those kinds of proposals as a national agenda, and there is little to draw from his small-ball legislative approach to suggest that he could succeed. Mr. Sanders is suddenly promising not just a few stars here and there, but the moon and a good part of the sun, from free college tuition paid for with giant tax hikes to a huge increase in government health care, which has made even liberal Democrats skeptical.

The changes didn’t go unnoticed. Following up on a post in Medium by a writer who goes by the handle The Broken Ravioli, Rolling Stone’s Matt Taibbi wrote a piece detailing changes made online to the article, moving it from glowing to lukewarm. Later, former Labor Secretary Robert Reich criticized The Times on Facebook, accusing it of caving in to Hillary Clinton interests.

Hundreds of Times readers expressed their disappointment or anger in emails to me on Tuesday and Wednesday, as well as on Twitter and Facebook. Many saw these changes as evidence that The Times strongly favors Mrs. Clinton’s candidacy. And some object to the practice of making substantial changes to articles without explaining that to readers – a practice sometimes called “stealth editing.”

Daniel Pereira of Alexandria, Va., wrote, “How in the world can the Times justify publishing a story and then, after it has been shared many times, changing parts of it wholesale to substantially change the tenor of the article, with no notice that a change had been made?”

And Sarae Pacetta of Upper Arlington, Ohio, wrote: “What goes into big changes like this? I’m familiar with corrections, but am curious about how an entire piece gets revised, especially with such a change in content.”

I asked top editors at The Times, along with Ms. Steinhauer and her immediate editor, for response. (The executive editor, Dean Baquet, also responded to Erik Wemple of The Washington Post on Tuesday night, and Ms. Steinhauer responded to the Rolling Stone piece. Both said, in essence, that the changes were routine efforts to add context to an evolving story.)

Ms. Steinhauer, in a response to my email, suggested that I speak to editors because “it was an editing decision.”

So, what happened here? Matt Purdy, a deputy executive editor, said that when senior editors read the piece after it was published online, they thought it needed more perspective about whether Mr. Sanders would be able to carry out his campaign agenda if he was elected president.

“I thought it should say more about his realistic chances” of doing that, Mr. Purdy told me. As first published, he said, editors believed that the article “didn’t approach that question.”

“There was a feeling that the story wasn’t written into this moment,” Mr. Purdy said. After the editing changes, he said, “it got to be a deeper story,” with greater context.

Three editors told me in no uncertain terms that the editing changes had not been made in response to complaints from the Clinton camp. Did the Clinton people even reach out?

“Not that I know of,” Mr. Baquet told me in an email. The article’s immediate editor, Michael Tackett, agreed: “There’s zero evidence of that.”

Everyone agrees that factual corrections have to be noted. As for editing changes in stories that are already up: I’ve written repeatedly that most do not need to be flagged to readers’ attention; doing that for scores of stories every day would be unwieldy.

But what about changes that affect the tone and substance of an article?

Three Times editors told me clearly that they don’t believe that was required here. These changes were “about nuance and depth,” Mr. Purdy said. In our conversation, Mr. Tackett referred to “the blessing and the curse of real-time capability,” and he said he made changes to developing stories every day.

Fair enough. But in this case, I don’t agree.

My take: The changes to this story were so substantive that a reader who saw the piece when it first went up might come away with a very different sense of Mr. Sanders’s legislative accomplishments than one who saw it hours later. (The Sanders campaign shared the initial story on social media; it’s hard to imagine it would have done that if the edited version had appeared first.)

Given the level of revision, transparency with the readers required that they be given some kind of heads-up, and even an explanation.

The Times has no workable way to do that kind of thing now. There are editor’s notes — but they are rarities, and therefore a big deal; they seem to be considered something to be avoided, if possible. But online stories elsewhere and blog posts everywhere routinely carry time stamps and notifications that a story was updated, often with an explanation of why. (Mathew Ingram of Fortune has offered some worthwhile thoughts about the value of this.)

So it can be done. And given the importance of reader trust in The Times’s credibility, the paper would do well to give some serious thought to how to do it here.

Update: A number of readers have made a point that I should have made earlier. The Sanders article was not a breaking news story, but rather a look back at his legislative record. Given its sensitivity and importance (it ended up on the front page on the morning of major primaries), why didn’t senior editors vet the story and make all the editing changes before it went online? Digital platforms, after all, are not a test run, and non-urgent stories don’t need to be pushed out as quickly as this one apparently was. I would also observe that the “context” added here looked a lot like plain-old opinion to this reader, and quite a few others.