It's too late for you now, but in the future, you can usually call Cathay and request an "upfare" to a mileage earning fare class. Or, if you are doing a phone booking, specify that to the agent on the phone. They are all too happy to take more of your money for the same seat.

Of course, ensure the fare difference is worth the miles you'll get.

I got burned many times on the fare class with various partners too, back in my pre-FT days. It's rather disappointing agents do not know only certain fare classes earn miles (or a percentage of miles), although most people are probably not as religious about their miles as we are here!