Have you tried to use multiple session factories ? One for the source User table and one for the runtime User table.
You could follow the programmatic api found in the Hibernate manual:
http://www.hibernate.org/hib_docs/v3/reference/en/html_single/#configuration-programmatic
I have used Spring's LocalSessionFactory to read in a configuration from a set of Spring files, run SchemaExport to an in-memory String[], then use the resulting scripts to pass to my DBA to apply on a production database.
You could do something similar, in the opposite direction. See
http://www.onjava.com/pub/a/onjava/2004/06/23/hibernate.html for an example program.
That is, once you run the reverse engineering tool, grab the results, save the xml file locally, load up a new SessionFactory with these new mapping files.
I do not think you could use the same session factory as the initial user table, because Hibernate validates all mapping files for referential integrity first.
There is no limit to the number of session factories you may use.