First of all; take a backup copy of your current installation!
Both the directory in the Tomcat webapps and the database!
Again, make sure that you have made a backup of your Tomcat webapp and the database!
Unzip the vp_installed_v4.1_20081113.zip anywhere on your disk
Start to update your VisionFlow database by running the SQL script 'upgrade_from_4.0_to_4.1.sql' located in the directory: '\WEB-INF\internal_docs\installed version\db_scripts\v4.1\Upgrade from 4.0\'. Choose the directory that match your database, MS SQL Server or MySQL.
Remove all files in the 'web-inf/lib' directory
Extract the content from "vp_installed_v4.1_20081113.zip" over your current installation.
Take the following files from your backup copy (1. above) and replace the corresponding files that was extracted in 5.