If you want to back up while using the database, you use the SQL command as follows:
BACKUP DATABASE TO ...
To restore the database, you use the main () method for org.hsqldb.tar.DbBackup or org.hsqldb.tar.DbBackupMain (version 2.3.2 or later) depending on the version of HSQLDB.
The commands are explained here:
http://www.hsqldb.org/doc/2.0/guide/management-chapt.html#mtc_backup
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