Recently I had a chance to be a part of setting up a Nutanix block (3 nodes). That block shipped with KVM hypervisor from the factory. Nutanix engineer was on site with us to do the first installation. Our first task was to replace the KVM with ESXi. We booted up all 3 nodes to do the re-imaging but for some reason only 2 nodes appeared on the management software. After some debugging we discovered that the Controller VM (CVM) on the 3-rd node was not working. There is a CVM console output file named NTNX* located in /tmp. From there we were able to see why the CVM was not booting up. For us the quickest way to fix the problem was to re-image the node manually with ESXi version.
Nutanix Controller VM console output under KVM