I've looked at this article (How to Display NetFlow Traffic from Vmware Virtual Distribution Switch to Physical Switch Switch Interfaces . ) but it's very outdated and requires manually adding hundreds of virtual interfaces. I've also seen this one, which is more recent: Add ICMP-only or VMware dvSwitch devices to the NetFlow Source Device - SolarWinds Worldwide, LLC. Help and Support. However it's still not automatically adding the new interfaces, because it says it doesn't support SNMP.
Edit:
I'm also testing it with VMWare NSX, which uses IPFIXv10, template 256 and 257. It looks like VMWare added some extra fields for VXLAN, listed here on their documentation: IPFIX Templates. Those 3 extra fields are:
IPFIX_VMW_TEMPLATE_FIELD(ingressInterfaceAttr, 2)
IPFIX_VMW_TEMPLATE_FIELD(egressInterfaceAttr, 2)
IPFIX_VMW_TEMPLATE_FIELD(vxlanExportRole, 1)
Also I captured some of the traffic, and they show as "enterprise private entry Vmware":

Message was edited by: Max Strzelecki