Yeah converting from one format to another that isn't completely compatible might be an issue in the future. Even how to preserve websites isn't exactly intuitive because as you saw the conversion to PDF was faulty, and doing "file" > "save as" would not yield the same HTML because the browser modifies the DOM. We have to start using formats specifically designed for archiving such as WARC for webpages: http://www.digitalpreservation.gov/formats/fdd/fdd000236.sht.... (relevant and interesting site in general, run by the Library of Congress)