Any recent experience with the "upgrade denied" message?

Last night .bomb really messed up the reservation record for an upcoming trip to Germany. I was waitlisted for an upgrade with miles (full Y --> C) and the overwater segment waitlist for the inbound disappeared, showing me confirmed in Y only. In addition, the outbound domestic portion entered UDU window and the upgrade was changed from waitlisted to denied. [My guess is a clash between UDU and instrument]. A call to the 1k desk nicely solved the inbound TATL issue as I had cleared to C and now that part of the record is clean. For the domestic outbound flight, the representative tells me that I am still waitlisted and nothing to worry about.

Is this still the common wisdom on FT? Just ignore the "denied" message?

Thanks!