The right order from scratch would be something like:
./make_clean.sh
./create_zones.sh
./create_configs.sh
Not the other way around!
sudo ./publish_zones.sh
./create_site.py
sudo ./sitepublish.sh
If, after this, https://workbench.sidnlabs.nl/zones/ is empty... Run sudo ./sitepublish.sh one more time.