Same way you might clean a floor. You clean all the parts that aren’t necessary for you to walk on, then you slowly clean the rest of it until there’s nowhere to stand, at which point you start walking on the cleaned parts instead and clean the remaining bits from there.
The part where the system steps off of the “dirty” part and onto the new, “clean” part is where things can get dangerous, which is why it wrests control from you and begs you to not power down while it does it. The actual “step” is taken when the system powers down and back up again. That’s the system shutting down the last of its old parts and stepping into the new parts.
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