You ever have something wrong with your computer and you reboot it, and magically it’s fixed? It’s like that. You didn’t actually “fix” anything, but sometimes when software runs long enough it gets into a buggy state that looks like hardware issues. There can be all sorts of software issues that can be fixed by sending commands to the spacecraft.
Alternatively if you know what’s broken, you can send commands to use what works to compensate for what is broken. For example if the craft thinks all the thrusters are working and if one is not, it may not move correctly. But if you update the controls you can have the remaining thrusters compensate for the broken one.
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