If it is not the LH (=Amadeus) reference number, it must be the Swiss internal reference (also a combination of 6 letters and numbers just like the Amadeus references). This can only be seen in the Swiss system, so you have to check with a Swiss agent (for more details see other posts in this forum.) My advice call Swiss to double-check and ease your mind.
BTW, on my recent trip, both the upgrades (done by LH from my M&M account for a Swiss flight) and seat assignments (done by Swiss agents and Cathay handling agent in HKG, repectively) do not show in Amadeus. It seems the systems do not update each other!? Also, the upgraded e-ticket could not be checked in by LH or Swiss, I had to have the ticket reissued at the Swiss Ticket counter. Even worse, on one booking, Amadeus showed the upgraded leg as "cancelled" without showing the upgrade. At the end everything worked out fine so. Just inconvenient.