I know this is an old thread and you have probably sorted it out now, but I felt it worth answering as it is something of a FAQ.
You bought an upgrade to HALion 6 from HALion Sonic 3 - the full version of HALion Sonic. You do not have a licence for HALion Sonic 3, which is why your upgrade will not apply. You only have the free HALion Sonic SE together with some content for HALion Sonic SE included in your Cubase licence.
There is no upgrade discount for HALion or HALion Sonic based on ownership of a Steinberg DAW. If you want HALion 6, you must buy a full licence for HALion 6 or Absolute 4.