The Tweaks "disappear" when the Kobo power off; as long as your unit only goes to sleep and does not power off, the Tweaks will remain active.
If you it does power down, you will have to reactivate them; ie, go to the Library view again.
When the Tweaks are installed initially, the files get moved from the .kobo directory to the "hidden" side of the Kobo and you can't see the files any more; they ARE there still though (and will work), just hidden from sight.
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