Try 'qmailctl cdb'.
This does not rebuild cdb from database and virtualdomains:
qmailctl cdb
Reloaded /etc/tcprules.d/tcp.smtp
Reloaded /var/qmail/control/badmimetypes.cdb
Reloaded /var/qmail/control/badloadertypes.cdb
Reloaded /var/qmail/control/simversions.cdb
Reloaded /var/qmail/control/simcontrol.cdb