I already reported a few weeks ago, that even though I made sure I booked flights with already existing upgrade availability and I did immediately see during the process of applying the coupons, that the upgrades were confirmed (and I was able to immediately select meals and seats), I was not able to check-in and get a boarding pass until I actually got the e-mail from RES OFFICE with the new ticket number! I believe this has always been the case with upgraded tickets, even with the old method. However there are indications that with the new method, the actual RES office emails don't arrive in a timely manner at all. I actually only got mine after I contacted Aegean's support channels after I realized I couldn't check in.
My other 2 flights I booked and immediately upgraded on Sept. 28th are still missing their new ticket numbers as well, exactly 6 weeks later!!
Unless I understood the post from intuition wrongly, he never got the RES office email either.

OttoMH I must add something to my previous post: It occurred to me that I have a faint memory of people reporting (under the old upgrade system at least) that such a booking when flown "partner airline first, Aegean second" would actually allow you to apply the voucher on the Aegean leg, after you had flown the segment with the partner airline first, since, practically, you then just have a booking with only an Aegean flight in it.
However it's not something I have ever attempted myself and I'm going off of my memory on something I believe I've read so I'd ask someone who's done it to confirm it (it still wouldn't apply in your case though, since you have the Aegean segment first, so that remaining LH leg will disqualify you).