We need to do the following steps for downgrade MySQL,
1. Change the MySQL version in /var/cpanel/cpanel.config file,
mysql-version=4.1 to mysql-version=4.0
2. Take old MySQL database bakup,
# cp -rpf /var/lib/mysql /var/lib/mysql.old
3. Remove the old database,
# rm -rf /var/lib/mysql
4. Remove old mysql binary,
# rm -f /usr/sbin/mysqld
5. Now run the script mysqlup
# /script/mysqlup --force
6. It will install MySQL 4.0 on server.
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