We used to have a manual that we shipped with the tarball. It was a PDF, generated with LaTeX, and manually converted to HTML. We switched to AsciiDoc format at some point (because LaTeX is unwieldy) which supported HTML rendering directly from AsciiDoc. As of 2.0, we put the manual directly in HTML on the website. But the site itself is rendered markdown. We've never really had stuff in HTML directly... it has always been generated in some form or another.
It's fine to update just the website 2.0 docs. One of the reasons for just putting the docs on the site is that the docs don't necessarily change significantly from version to version... so it's not necessarily sensible to a different copy in each release. So, just updating https://github.com/apache/accumulo-website is fine. We can always backport to the AsciiDoc version for 1.9 if necessary.
