I'm not sure if I can offer any particularly useful advice, but I can empathise because I'm in a similar situation right now. Likewise, I only ever resort to using Expedia when I haven't been able to book an itinerary directly with the airline.
In April, I booked MEL-SIN-FRA-BUD (departing Dec 22nd) and ZRH-SIN-MEL (departing Jan 17th). All under one PNR, all in Premium Economy except for the FRA-BUD leg, with a mix of carriers (SQ, LH, LX).
In July, Expedia advised that LX had cancelled the ZRH-SIN flight on Jan 17th and so I needed to make an itinerary change. That's when all the problems began. The first agent who handled the change rebooked me into Economy for ZRH-SIN-MEL on Jan 18th, despite assuring me that it would all still be in Premium Economy. I then noticed the error on the eticket. For the past five months, I've been trying to make them fix the mistake, to no avail. They just kept telling me to "check back again in 72 hours"...for five months. The flights remained "waitlisted" during that time. And now, the SIN-MEL leg has disappeared from my itinerary.
I finished an online chat with Expedia a moment ago and they're now telling me there's no availability for ZRH-SIN-MEL between Jan 18th and 29th - great
They told me to either check back in 72 hours (again...), or to take a full cancellation and refund. In any other situation I would take the refund and run - but I'm due to leave in 5 days, and I'm travelling to spend Christmas in Europe with loved ones.
In my case, the issuing airline is LH, and fortunately my outbound MEL-SIN-FRA-BUD still has everything correctly booked. I've spoken directly with LH and they advised that they can "take over" my ticket once I have started the itinerary. So that's exactly what I'm going to do: fly out as scheduled, and then immediately call LH to resolve the problem. It's risky, but I sense that it's my best option right now. Fortunately, I have friends in Zürich whom I can stay with for as long as I need to while I try to sort out this mess.
I've tried two tactics other than the Expedia call centre, which you might consider as well:
(1) DM Expedia at their Twitter help account (ExpediaHelp). I found that the staff running that account seem to be a bit more efficient than anyone I've dealt with via their call centre or online chat, but YMMV.
(2) Call the issuing airline, explain that you are having trouble getting Expedia to fix the problem, and ask if they can offer any suggestions. That's how I found out that LH does have the ability to take over my ticket.
I would also be interested in hearing from anyone who has experience with resolving these kinds of issues with Expedia! Next time I will go out of my way to avoid booking flights with them, even if it means being a bit creative with routings to get to wherever I need to be
*Update: I ended up just taking the full cancel/refund, as a perfect F redemption became available on EK. It took a few tries to get a competent Expedia agent who could help me arrange the refund, but I lucked out - if you can somehow get hold of Richelle in the Phillipines call centre, she's the one to go to. She also helps to run the ExpediaHelp Twitter account, which may actually be the best chance of reaching her given the random nature of the phone lines. She kept me on the line while she called LH so that I could listen in on their call, and then immediately arranged the refund for me. I would have done a chargeback if it had not worked out like this.