Clouds are made out of water particles suspended in the air. They move with the flow of air they are suspended in. If an airplane flies through a cloud, it disrupts the airflow, and the water particles move in the distrupted air flow ([see here](https://www.google.com/imgres?imgurl=https%3A%2F%2Fi.pinimg.com%2Foriginals%2F29%2Fee%2F7b%2F29ee7bcfe94cf5b91bb82942debdbc7f.jpg&imgrefurl=https%3A%2F%2Fwww.pinterest.com%2Fpin%2F286119382548759257%2F&tbnid=Bu2NNdVUYqo9JM&vet=12ahUKEwj-qfHPp5_tAhUJD60KHdsYDbEQMygAegUIARCyAQ..i&docid=QdZCB8ozT92HPM&w=450&h=302&q=aircraft%20cloud%20wingtip&ved=2ahUKEwj-qfHPp5_tAhUJD60KHdsYDbEQMygAegUIARCyAQ)). The water particles are still all there though. The plane doesn’t absorb them or anything, so once the air settles down again they be more or less in the same place they were before.
To make the hole the plane would have to be scooping up all the cloud it touches and take it away with it. That certainly is not happening. Basically what happens is the cloud separates and moves out of the way as the plane flies through it and then the cloud moves back again. The cloud is effectively no different from air (except that you can see a cloud) so it behaves exactly how air would.
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