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Do you have VMs connected to logical switches in every host?
As mauricioamorim said, ESXi host joins the VNI (say 5000) in the following two cases:
- Host has a VM connected to a logical switch with that VNI (5000).
- Or host has a VM which is connected to a different logical switch (VNI 5001), but needs to talk to a VM running on another host connected to that VNI (5000).
If none of the above is true, you won't see this ESXi host in VTEP table for that VNI.