I noticed this in trac last night and there is that change in wpmu-functions.php file. I am looking to see where some features of existing installs might "break" with the change and prepare for them. So please correct me if I am wrong in any of my assumptions below:
1. For main navigation I use the <?php switch_to_blog('1') ?> for sub-blogs of WPMU installs used as CMS. The main navigation won't be affected.
2. For an old WPMU install, I put BP in blog_id_2 by adding the following in wp-config.php:
define ( 'BP_ROOT_BLOG', $blog_id ); where $blog_id is 2 in that install. Since $blog_id is WPMU function and not BP, then I don't need to change anything when I upgrade this old install later on to stable WPMU 2.9 and BP 1.2.
3. I have to check plugins especially the ones in my mu-plugins for references to $blog_id and replace with new $_blog_id - and see if they work when I upgrade the development install later this week to trunk.
Feel free to correct me or add to checklist above.