You did not say which platforms you are using.
If I understand correctly, there is nothing in the database you want, so why not just uninstall and reinstall from scratch?
If you can experiment I would attempt to follow the JIRA database migration process
1) shutdown JIRA
2) create a new database
3) remove the dbconfig.xml file
4) Restart JIRA
JIRA should take you through the database initialization procedure
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