I feel your pain. This happened to me last week - logged on to the Qantas app and found that 3 out of my 8 flights on the itinerary (all QR long haul flights in business) had just vanished off my itinerary - despite being ticketed. Absolutely no communication about this from Qantas.
Made 9 or 10 calls (all to call centres in Fiji/SA/Philippines - for reference I'm Qantas Gold) - got told so many different, totally absurd things. One lady even said it was MY JOB to ring Qatar to get it reinstated...out of desperation I even tried this - and was told, expectedly, that it was a Qantas ticketing issue. Tried FB Messenger and Twitter to no avail. Was starting to become super depressed that the holiday I booked a year ago was looking like it would be off due to no fault of my own......
As a last resort, after trawling these forums, I tried the "email the execs" option. Lo and behold, within 48 hours, I got a call back from a real human in Hobart, explaining that a QR flight time change on my very first leg (which I knew about but was so minor I'd ignored it...literally the flight was scheduled to land 5 minutes earlier and had a different flight number) led to that initial flight being reticketed by Qantas on a different ticket number.....but without any of the remaining flights. For some reason Qatar Airways picked up on this, and ??assumed the other 3 long haul segments were not needed and cancelled them.
After a further 48 hours, I got a second call back from the guy and now all my flights are there again, all ticketed (under one new, unifying ticket number). While I perhaps don't fully understand the exact nature of the stuff up, he even said to me my case would be used as a 'reference' if this happens again (who knows if he's making that up hahaha).
All I can say is that this was an incredibly stressful experience and I'm at the point of expecting another stuff up before the itinerary begins in May