VDOMs have quite a number of dependencies that need to be deleted before you can get rid of the VDOM itself. Below is a useful little script that goes through all the sections and purges them so the VDOM can be deleted. Adjust it as needed.
This script needs to be run interactively. In other words you cannot copy and paste the whole script. You have to acknowledge each purge command.
## Purge all VDOM specific configuration
config vdom
edit
config firewall policy
purge
end
config firewall policy6
purge
end
config firewall vipgrp
purge
end
config firewall vip
purge
end
config firewall addrgrp
purge
end
config firewall address
purge
end
config router static
purge
end
end
## Assign any interfaces used by the VDOM back to ROOT
config global
config system interface
edit
set vdom root
end
end
## Delete any VDOM Links
config system global
config system vdom-link
delete
end
end
## Make sure all admins are assigned to the root VDOM
config system global
config system admin
edit
set vdom root
end
end
config vdom
delete
end
