Upgrading from an earlier version of Sakai typically involves a database conversion (for which scripts are supplied with the release), an update to custom skins and possibly changes to any custom code.
Please run ALL the scripts from your original version to the version to which you are upgrading. There are two sets of database upgrade scripts, one for MySQL and one for Oracle. Use the appropriate scripts for your database type.
Sakai also includes data and schema conversions outside the standard scripts to address data integrity issues for assignments, content hosting, email archive and migration to GradebookNG (the new default Gradebook. Gradebook has been renamed Gradebook Classic as of Sakai 11). Below is a quick summary and overview of the process for each tool.
Please read this blog post by a senior Sakai developer.