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
This is corrected by