well, I don't know if there's a better way to do that, but here's how you can do it:
reload nagios with just one dummy hostgroup+host+service.
Then reload nagios with your normal config.
This will do a fresh start for all your services (you'll see them as "pending" without any old status), thus erasing your performance stats.
note: as a consequence of that, you'll lose some service history, status ...etc. Don't do it if you might need it