First of all; take a backup copy of your current installation!
Both the directory in the Tomcat webapp and the database!
Again, make sure that you have a backup of your Tomcat webapp!
Unzip the vp_installed_v3.2.1_upgrade_from_v3.2_20080221.zip anywhere on your disk. Do not use the "zip-archive program" that is included in Windows, it has some major flaws with long-names. Use Winzip or anything else that you can trust.
Start to update your VisionProject database by running the SQL script 'upgrade_from_3.2_to_3.2.1.sql' located in the directory: 'WEB-INF\internal_docs\installed version\db_scripts\v3.2.1\Upgrade from 3.2\MS SQL Server'.
Remove all files in the 'web-inf/lib' directory
Extract the content from "vp_installed_v3.2.1_upgrade_from_v3.2_20080221.zip" over your current installation.