It was discovered that the traitor among the Vegapunks is a person who plays an important part among the Vegapunks. This makes it difficult to confront them.
This article contains spoilers for One Piece Chapter 1078, “Escape Limit,” written by Eiichiro Oda, Stephen Paul, and Vanessa Satone. Viz Media
The most significant event in One Piece Chapter 1078, “Escape Limit,” was the unveiling of the traitor in the Vegapunks. It was revealed that it’s been York the Greedy who has been arranging things on Egghead for the last three months. The nature of her involvement makes this situation much more complicated than if it had been any other Vegapunk. This includes Stella.

If it was any other Vegapunk, the solution could have been easy. The Straw Hats will need to do is abandon them to fate in the hands of the World Government or destroy them in their way or something similar to the way Kanjuro Kurozumi was handled. Since most of the Vegapunks are only interested in analyzing and gathering data, it won’t be a huge loss if something happened to any of them. York, however, plays an essential role among the Satellites.
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York is not responsible for the analysis or gathering of information. York is instead responsible to fulfill all bodily functions, like eating and sleeping. York is the source of energy for the other Vegapunks to continue their work. If she’s unable to perform her duties or her satellites are unable to function, they may be unable to continue their work due to exhaustion or starvation.
Other Satellites might be able to eat and sleep independently, however, it’s not confirmed. It also might be difficult for the ones which don’t have human bodies; the more robotic ones, like Pythagoras and Edison might need someone to eat on their behalf. Even if they dispose of York, Lilith or Atlas may still require enough for both of them as well as Shaka.
If other Satellites require York to live and live, then the original plan doesn’t change in any way. All seven Vegapunks from Egghead will be transported by Straw Hats on their way to the next location. They’ll now have to take the Greedy one prisoner, rather than their guest.

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The whole thing depends on what happens to Pythagoras or Shaka. Both seem to be murdered, but One Piece fans are familiar with second-guessing apparent deaths and expecting a fake out. If these two are either alive or can be restored, then York can be given as much of a second chance that any villain would get. If they can’t, then she’ll be considered an unredeemable creature and handed whatever is thrown at her.
What is going to happen now that York was revealed to be the traitor is anyone’s guess. York may be brought aboard the Thousand Sunny as a prisoner, taken in by the World Government, or simply killed off. This last option may not be the best depending on her significance.