So, a minor update here (if anyone else has the same question).
I spoke to several agents on the Senator line and they do no longer allow double upgrades, not even at check in. She said they can do it at the gate to resolve an issue but if you upgrade from Y to PE you cannot purchase an upgrade to J.

With that info in mind I chose to buy a cash upgrade from Y to J on the return flight from Singapore to Zurich, it has been confirmed and I can chose a seat. Still waitlisted for upgrade on the outbound, so it was a diffrent segment I upgraded using cash. However Swiss refuses to reissue my ticket. I claim it should be reissued to reflect the confirmed upgrade. Thet say they cant reissue and that it doesent matter as upgrade is reflected in their booking system. Having travelled quite a lot Im not 100% satisfied with that answer bc there seem to be conflicting reports even within Swiss. Two agents have put the reservation on que to be reissued and then nothing happens in 48h hours and another call.
If I request receipts it still says Economy on that segment. Feeling like I will lose the e-vouchers, the cash paid for the confirmed upgrade AND the possibility to fly since when I try to check in there might not be a ticket. I do have an e-ticket and that one says Economy.