Do you have direct access to the etherpad DB?
Otherwise, look for the readonly-links, but there you wouldn't get the "comments" = chat history, which you usually anyway have to load manually.
So probably, you'll need a custom export script. John who runs PrimaryPad might have something to sell, or if you have your own coders you could create a custom pad template with your wanted formatting, and add or dig out a feature to fill in that template with also the chat history.
I'm an (in)active committer to http://github.com/ether/pad and I'm fairly sure there doesn't exist any bulk export features. Anyway, what good is export without import.
Upgrading is painless -- etherpad has built in features to upgrade the database as needed, so just pull from the git repository. But perhaps pick a release tag like 1.0.1 to stay clear of the bleeding edge / trunk.