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I am new to Kali-linux and I am using it from a USB, my problem is when I shut down my computer and downloaded scripts or changes I have made are gone

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That is probably because you are using it from Live mode which is only useful when you want to test few things out. It does not save anything

You can always look into this persistent kali usb

Rob
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  • Questions about operating systems, their utilities, networking and hardware, are off topic here. [What topics can I ask about here?](https://stackoverflow.com/help/on-topic). Do not answer off topic questions. [answer] – Rob Apr 04 '21 at 12:07