Thanks for the replies guys. Basically I ended up landing in KUL with the plan to go straight to the Royal Jordanian desk/office and sort it out. Of course, it was closed!

Ended up going to the airport information desk, standing up for two hours on and off on the phone with the Kuala Lumpur town office of RJ. Thankfully, found a really great guy there, Kevin. Honestly the first person I've been able to speak to from RJ who knew this ticket, even joked with him about it! He said most of the staff don't know how it works because it's the kind of ticket they see "seldom, maybe once in a lifetime". Explains why normally I'd give the ticket number and they wouldn't know what to do with it, put on hold for 10 mins and then look it up fine

Anyway long story short after about an hour Kevin was able to fix everything up again. What had happened was my original date change hadn't been done properly, and still showed 27th May (which I'd obviously missed). Strange that it was showing up on BAs app as 31st before it vanished, so I guess there are two different systems and they only knew to change one?

I don't blame RJ staff because naturally they are not used to it, but something to bare in mind if you book this ticket through them :-) BA were always helpful but twice said they couldn't make changes because they weren't the ticketing airline, is this correct?

In case it's useful to someone, the number of the KUL office is: +60 2148 7500. Ask for Kevin! :-D