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What happens to the electrons that were knocked out where do they go? What happens to the electrons in the higher orbitals that are knocked out of orbit, I am sure they release photons as well as they are replaced, but also when an electron is filled in, there is a missing electron in the outer shells, now they are not electrically neutral or ionized. What happens then? What are those implications?

Texts explaining the x-ray process only discuss the knocking out of an electron as it is hit by an accelerated electron and the release of photons when an electron from a higher orbital replaces the knocked out electron. There's no follow-up explanation as to what happens to the spot left by the replacement electron. Which electron fills it up?

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Your sample is in some way connected to ground. When the sample loses an electron, a free electron from ground can conduct through the sample and fill the hole. If your sample is insulating, it's possible to remove the electrons faster than conduction can replenish them, so you do end up with a charged sample.

When performing XPS (x-ray photoelectron spectroscopy), which uses this electron-ejecting phenomenon, a flood gun is used to quickly restore neutrality in the sample.

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