There may have been a firmware bug like that, I don't remember clearly because I don't use hyphenation myself.
A factory reset will erase any and all changes made by KoboRoot.tgz unless some modder turned evil and installed the mod to your recovery partition too.
If you're referring to my mod which exposes the hyphenation files to the user partition so you can edit/replace/rename the hyphenation dics via USB... it obviously does not survive a factory reset; nor do you need one, if you lost the original dic files you can just extract them from the Kobo firmwareupdate tgz.
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