This was suggested I post the issue on these forums after not finding a solution in the BP forums. Ref: http://buddypress.org/community/groups/how-to-and-troubleshooting/forum/topic/how-to-update-the-wp_bp_user_blogs-table-to-reflect-current-blogs-and-blog-administrator-owners/
Something has gone wrong with my superadmin and his owned sites on the network. For some reason when I ran an upgrade or deactivated/reactivated Buddypress the superadmin would gain sites that weren't his and lose sites that were...in the wp_bp_user_blogs table which houses blogID and its admin user_id.
I finally figured out why superadmin was gaining blogs was because superadmin was a member on those other users' sites. I used the fantastic plugin Simple User Management to fix this.
I tried using SUM to make the superadmin the administrator of the missing sites but it doesn't list the missing row back in the wp_bp_user_blogs table. This site has always belonged to userid=1 so I don't know why it's not taking. There might have been other adminstrators during the years but they are not admins anymore.
So I'm trying to see what I can do to manually force that table to rescan the network and relist the correct blogIDs and user_ids in that table which is responsible for helping display sites belong to users and also displaying sites in admin bp tools. If the sites aren't in the table, they don't show up on the site.
The missing sites are not set to private so that's just another tidbit.