2.0.4 to 2.0.5 database changes

I’m running multiple WP blogs for different faculty off of a single MySQL database, using different table prefixes for each blog. The documentation on the 2.0.4 to 2.0.5 upgrade includes “you will be prompted to click on the link to upgrade your database as there have been changes to the database scheme between 2.0.4 and 2.0.5”.

If I upgrade one of the faculty blogs, will all of the others be broken? Do I need to plan on upgrading them all at the same time (like 3 in the morning some time)?