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It all depends on how much javascript is needed to handle navigation, how the webpages are actually laid out (actual html structure and tags used) and etc. Things like a table of contents and keeping chapter order are standard in epub.
Without seeing the website page source and css, there is no way ti tell if this would be easy or hard.
That said, most browsers support some type of website download and archiving that can be used by the browser when offline. That would be much easier way to achieve what you want.
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