/opt/bitnami/mysql/bitnami/my.cnf is a symbolic link to
/opt/bitnami/mysql/bitnami/my-medium.cnf in your instance. This file is being include from the main config file at
/opt/bitnami/mysql/my.cnf using the line below
If you modify that file, changes will persist over instances restart as the symlink will be the same. In case you resize the instance, the symlink will be updated and your changes won't take effect. You can either modify the
my-medium.cnf file, or remove the include from the main
my.cnf file and add your custom config to the
/opt/bitnami/mysql/my.cnf file to ensure that an instance resize won't have any effect over your custom config.
Hope it helps,