Re: Howto upgrade WPMU with BP running
As JFcarter suggests, you should make a backup of your database before beginning this process. Your BuddyPress data should be in the same DB as your WPMU data. You also may have some image files in other locations, so back those up as well. Finally, be carful of what you delete in wp-content. If you have any customized themes, or 3rd-party plugins, you will want to make sure you have a backup just in case.
Now, upgrading WPMU: Unless this issue has been recently fixed, you cannot use the auto update feature to upgrade WPMU 2.7.1-beta1 to the public release version of WPMU 2.7.1. This is because the upgrade script “sees” WPMU 2.7.1 = WPMU 2.7.1, meaning it does not upgrade you from beta1 since it thinks you are already running 2.7.1.
So, you need to do the old manual upgrade of WPMU following these procedures.
Upgrading BuddyPress: follow these instructions.