I've just discovered that when using
SchemaExport export = new SchemaExport(conf);
generates random foreign key constraint values to drop and does not use the constraints that are existing in the database. This means that I cannot drop the db anymore, so I had to move back to Hibernate 4.2.0.
use random existing DB, try to execute drop script and you will receive sql errors while removing constraints.
4.2.1, MySQL 5.5