This is very old, but does roundup-admin init do the trick?
It seems like it calls: tracker.nuke() which should remove the old
database.

You may need to rm -rf db/*

to remove the msgs and files subdirs where files contents are stored.

In newer (1.6) releases the database backend is stored in config.ini
and not in db/backends so I think even an rm -rf db will work without
losing anything important.