First, a little background. I have a set of Java applications, some based on JPA, some not. To create my databases I am currently using Hibernates schema export to generate
Liquibase handles it quite fine. It looks at your database at the current state, finds unapplied changesets and generates an SQL script with update command in sql output mode.
Using a proper database migration tool instead of Hibernate generator is the way to go in any case, sooner or later you'll end up with a situation that Hibernate does not support. For us it was dropping an unique index and replacing it with another. You can also enable hibernate.hbm2ddl.auto=validate to feel safe about the compatibility between database structure and entity beans.