ESXi is definitely not comparable with Windows (on which I agree with you with the clean installation) and I'd recommend you Upgrade the ESXi host rather than installing it. In case you want to install (preserving the VMFS of course) anyway, you will have to reconfigure all settings (network, NTP, users, pools, ...) and then need to re-add the VM's to the inventory by right-clicking the .vmx files in the datastore browser.
André