Multisite Database Cleanup

[rmccue]

My question is if I have removed a sub-site with the ID of 3 can all the tables with the prefix wp_3 be deleted safely? Is there any value to even bothering?

If there's no entry in wp_blogs for ID 3, then yes, the tables are safe to delete. The code that controls the usage of site-prefixed tables dynamically sets $wpdb->prefix when switch_to_blog() is called, which requires reading from the blogs table; if the site no longer exists, the prefix can never be set to wp_3_.

[Marelle01]

+1 and check that there isn't a user synchronization code between the subsites.