I installed ESXi 6.5 from a 32GB SD card (inserted into hyper-visor motherboard usb port) and chose to install it on the same card during installation. I set the pass through on my LSI controller & USB controller, and applied a license. I rebooted and these changes retained/stuck.
However, I then added datastore1 (ssd) and uploaded backed up VMDK'/VMX's from prior EXSi 5.5 environment to this datastore and registered the guests with ESXi 6.5. All VM's were running fine at this point.
I shutdown the guests VM's and rebooted the ESXi host.
To My surprise all the VM's unregistered themselves, but the license and pass-through settings retained.
I re-registered the VM's and rebooted ESXi host again, same result.
Any help to point me in the right direction would be greatly appreciated.
EDIT: My problem at this point is not being able to toggle passthrough off for my USB controller, which might be causing this, due to it being mounted in RO and I am not able to edit the /etc/vmware/esx.conf file either to disable it by changing the device from "passthru" to "vmkernel". I will schedule more downtime to try serverfault.com/questions/791355/
UPDATE 11/30/18: Scheduling to reinstall ESXi 6.5 as I do not have a backup of the esx.conf file.