Earlier this year I wrote a small guide on what to do when you're experiencing character encoding issues after upgrading MySQL to version 4.1 or higher. Now after a large combined effort with JirkaRybka a documentation page is set up in the Troubleshooting FAQ: MySQL 4.0 -> 4.1 migration.

This guide includes background information, a description of several issues when upgrading MySQL and a solution for each problem. You no longer need to manually change update.php (cfr. my earlier guide) since a stand-alone script was written that works for Drupal 4.7, Drupal 5 and Drupal 6! This is very important since Drupal 6 will require you to have MySQL 4.1 or up, if you're using MySQL of course, and this will make upgrading so much easier, saving people a lot of precious time debugging. This documentation and the script are all a combined effort of JirkaRybka, Heine, Acert93 and myself.

You can check the original request by Acert93 to provide more information on this issue and see how this documentation came to be.

This night the host of a client upgraded from MySQL 3 to MySQL 4.1. It is a known issue that his might bring problems regarding character enconding, resulting in special characters (like acute accent or umlaut) or getting defaced. Some of these issues can be resolved quite easily, for instance the user error "Illegal mix of collations". We'll first look into what happens behind the scenes when upgrading from MySQL 3 or MysQL 4.0 to MySQL 4.1.