Question: I have been working in a research position in a DOE lab in the United States for the past year or so, and my mentor wrote me letters of recommendation for my graduate school application. I have been, to put it bluntly, worse at my job recently than I had been when he wrote the letter, and I would quite like to leave soon as:

* It has always been a poor fit for my interests, and I am rapidly losing the motivation to continue;
* I have not been challenged/learned anything new for months, and I do not have the discretion to change this;
* I am not vital to any of the ongoing projects in my group;
* I have saved enough to support myself through matriculation.

I am very worried that, given my recent job performance, if I leave soon, my mentor might try to contact graduate programs to which I submitted applications 1+ months ago to give an update on his impression of my character/abilities/etc. Is this a real possibility? If so, how would graduate schools react, receiving this so long after submission, or if they've already accepted me?

Answer: 
Anything is possible, of course, but (warning - opinion coming), I think it would be very unlikely. First, I doubt that your mentor would do that, though I don't know the person so can't be definitive. I would not, anyway. Second, if you have been accepted (and told them you are coming) you have at least an informal contract that is unlikely to be broken. In some places it would likely be against regulations to withdraw an offer after acceptance. But again, I suppose it is possible that it would happen.

However, you might be questioned by your mentor or others about this, so be prepared to give an honest reply. People learn as they live and they change their minds about things. Other people generally understand that and accept it as long as it doesn't cause disruption. 

But I think your worry is probably based on very little. (Sorry about all the "weasel words" here.)
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I can only speak for myself, but I would have to be VERY angry before I would take the time and do something as drastic as this. At worst, I can imagine someone rescinding their letter without sending an update, but even that would be far beyond something I would consider doing for an average case.

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> If so, how would graduate schools react, receiving this so long after submission, or if they've already accepted me?
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If the new letter described some really egregious conduct (e.g., fraud, stealing), this would certainly affect the decision. For the sort of minor matters you describe, I think it would reflect poorly on the sender, though whether it also reflected poorly on the student (particularly to the point of changing the decision) is hard to predict.

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> I have been, to put it bluntly, worse at my job recently 
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Unsolicited advice: consider leaving soon (or rededicating yourself). It's possible the problem hasn't even been noted yet, and people are unlikely to be offended by your decision to pursue other paths. But if this continues for months, you will likely burn a bridge.