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I made a persistent Live USB with the usb-creator, and I was wondering if I can just update as one normally would, or if there are special procedures I need to take.

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yes of course . if live image on a usb ( there is space ) you can update as a ubuntu on hdd.

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There are no special procedures. But your setting would not be saved if you have not made a persistent Live USB. You can read more about it on Ubuntu Wiki.

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I've been able to update many things, but updates affecting the Linux kernel and its modules don't seem to happen correctly on those sticks I've created this way.

If I'm not mistaken, the reason is that the kernel being booted isn't with the rest of the root partition, but stored separately on the stick.

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