I'm guessing you might have been in a rush just to ticket something while this was fading away, but you can (well could at the time) definitely route CAI-AMM-DOH-HKG on the OW tool, but it had to be done rather manually. It would however ticket as a connection in AMM. Just for future reference the Booking and Pricing sticky thread is really useful for getting advice if you get stuck in the OW Tool on something like that.

Generally it seems too late to change the ticket now because of the reprice, but if you'd have mentioned that problem last week I'd likely had advised to get it changed to CAI-DOH-HKG and drop RJ, but guessing you're on a QF ticket and they've been saying they're not going to make routing changes on these ex-CAI tickets anymore because of the fare change.

I've never attempted separate ticket through check in with RJ, they may or may not do it so be prepared to buy the Jordanian visa and be pleasantly surprised if you don't have to. Since Jordan is on the high side for visa costs, it is a bummer to buy it just to go re-check in but they aren't required to through check luggage. QR however will very likely do it if you do end up checking in in AMM, so you won't have to retrieve it in DOH.