There is no way to go directly from ePO 3.6.1 to 4.6, you would need to go through ePO 4.0 first up to 4.0 patch 7.
Then from ePO 4.0 Patch 7 you can run an upgrade to ePO 4.6
You can only preserve settings in this scenario by using the upgrade path provided by the installer.
if you can do the upgrade on existing hardware/OS then yes clean install would be preferable.
I understand that it is possable to build a new server,New Epo Box and transfer exsting settings from3.6.1 too 4.6.1
this has been done on numerious occasions, and not go through the step by step version by version uprade process you suggest.
i was just looking for known errors to be awrare off
but thank you for well intentioned input.