Cambo

OTA=Online Travel Agency

For CX, I always call the Hong Kong number. Other helpdesks tend to be pretty clue- and useless for anything more than the run-of-the-mill items.
Having your own VOIP line makes these long distance, long duration calls more affordable. When I call the CX Hong Kong helpdesk, it does cost me EUR 0.04, independent how long the call takes.

Can "segments" be removed from bookings: Yep.

Where the general public can only book fixed journeys, travel agencies (and the airline helpdesks) can (technically) add (about) whatever segments they want to an itinerary (and remove these too). Of course, only when matching the rules and when segments are available. This way, in the same PNR, you can have several parallel travel options waitlisted, until one option clears and one contacts the travel agency to ticket that specific option and remove the others.

In this case, it seems, the OTA did not only add some segments waitlisted, though also removed the original segments. Once removed, these segments are gone from the PNR. Reinstating would be possible against the current availability/pricing/rules.

However, when you have good standing with the airline, they might be willing to open-up a cheaper fare bucket and add from those to the PNR.

For your case, I don't expect this lower buckets opening to happen, given you booked through an OTA (signaling "go for a low price") and avoided the direct airline's offers. Such an action is an indication of shopping around and not a loyalty item towards the airline, so why should the airline be loyal to you ? Especially, when the sales situation is already in favor of the airline.

Given the original segments are already gone, I don't think, "being friendly", etc, will help in any way.

In case the original segments are still there, you may have some (minor) chances, to get things arranged, even when booking through an OTA. When contacting the airline, they will not touch the itinerary, though, you can inform what options are available, so you have more information to instruct your OTA what to do. When an OTA gets clear information of what can be done, because it's available, etc, you have far more chances the OTA is willing to dive into this, then, when the OTA has to sort out the options themselves, contact you, etc.

The OTA business model is "sell and don't bother", OTA margins are simply too small to have their staff diving into all kinds of change options. As such, my suggestion to "prepare" with the airline what is possible, and let the OTA execute the changes.

Officially, airlines don't have to help you with OTA requests, so, it'll need a lot of social "manipulation", to get the helpdesk to look into your request as well get the info you need to direct the OTA. And at the other side, it'll need social skills to get the OTA prepared to dive into your request and perform the changes, since that's not matching their business model.

Unfortunately, for your case, I think, it is not going to work, the original segments are gone, and you have no loyalty standing at the airline.

Your hopes: Maybe the waitlist clears or, you can manage to find a last minute offer, somewhat suiting your needs.

Or so to say, better book direct with an airline, unless you have very specific travel requirements, like mixed cabin classes, mixed alliance, all in one PNR.