It will be overwritten on each upgrade, but that's why you keep the KoboRoot.tgz that you create, so you can re-apply the change after each firmware upgrade. For best results, which I know may not be ideal but should be better than what Kobo does by default, you check the driver option to override the content file language, replace the built-in hyphenation dictionary with a newer one, and re-apply the hyphenation update after each firmware update until Kobo finally delivers a good hyphenation update on their own. Obviously, if you don't like the results even with the updated hyphenation dictionary, or if hyphenation isn't worth the inconvenience of applying a patch after every update, you can just go on with the custom CSS to disable hyphenation everywhere.
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