Like Ryan mentioned:
session.createSQLQuery("BACKUP TO \'" + file.getCanonicalPath() +
"\'").executeUpdate();
was just missing. And for me I had to escape the '-character.
Thank you for the basic approach, which led me to my solution!
For linking, my special problem was also getting from entities to hibernate
Sessions::
https://groups.google.com/d/msg/h2-database/ri3SiqWezkM/UpVR4t6vFAAJ
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