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Numerous users expressed outrage at the change, which had been due to come into effect in January, and said they intended to quit the service in response.
But in the face of the backlash, the company has performed a U-turn and says the change won't go ahead.
"We've heard your concerns, and we apologize for any angst we may have caused," CEO Chris O'Neill said.
The original plan had been for all users' accounts to have machine learning functionality enabled by default, with employees able to view notes when necessary to review and provide oversight of the software.
But the company is now changing tack: "We will make machine learning technologies available to our users, but no employees will be reading note content as part of this process unless users opt in," it said in a blog post published Thursday.
The app is popular with journalists, among others, and there was significant alarm at the idea of Evernote employees being able to read often-sensitive notes and documents.
I keep a lot of sensitive stuff in Evernote, including interviews with anonymous sources. This is bad.
- Steve Kovach (@stevekovach) December 14, 2016
{the sound of 100 reporters scrambling at once for an Evernote replacement}
- mat honan (@mat) December 14, 2016
That said, some employees do still have the ability to view notes in certain "limited" circumstances - such as if the company receives a warrant from law enforcement, it needs to investigate terms of service violations, or troubleshooting. "The number of employees who are authorized to view this content is extremely limited by our existing policies, and I am personally involved in defining them," CEO Chris O'Neill wrote in a blog post.
So if you're hoping for a service where the operator will never be able to see your content, you're still going to have to look elsewhere.