I am going through a similar dilemma. Before you do anything, I recommend taking a look at the Interoperability Matrix first. VMware Product Interoperability Matrices Simply put ESXi v5.0...
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I am going through a similar dilemma. Before you do anything, I recommend taking a look at the Interoperability Matrix first. VMware Product Interoperability Matrices Simply put ESXi v5.0 will not be supported on vCenter v6.5 version, as ESXi v5.5 is the last one to be "included" under that formula. So, review your versions carefully, and your options, and then either purchase another vCenter license to support your older VM Hosts, or upgrade all v5.0 hosts to at least 5.5.0 U3 and extend your life cycle, but probably only until v7.0 vSphere shows up.... Regarding your question about upgrades - You can either upgrade, then migrate the license to another host, Or, Not upgrade at all. The old licenses *might* still work, for just the reason you are describing, (bring up new host on 6.x eval , migrate VMs, decommission 5.0 box, upgrade license, apply to new host) but probably only for a very limited time (60 days or less in total.) You ought to be able to connect the new vSphere hosts under eval licenses, and then push the VMs over, and then apply the new upgrade license once the migration has completed, and the 5.x box is offline. I think that I would put a ticket into Support to validate this method, unless you have time to test the theory yourself....