Possible gearbox problem, r53 cooper s

Hi All. First post and not a happy one.
Last year my wife bought a very tidy cooper s convertible (made Dec/06) with sensible mileage, and good history. In fact it had been serviced 3 times in the last couple of thousand miles prior to us buying it (one of these being a pre delivery service when we bought it)

Mot was due a couple of weeks ago so I booked it in. It however developed a noise the night before that sounded like a stone rattling around caught between the brake disc and disc shield. The next morning my wife went to go out in it but quickly returned saying the noise was worse. I took the wheel off (front left) and was greeted with the sight of a badly split inner CV joint boot, and a lot of grease that had spilled out.
I explained to the mot garage about the problem and asked to fix, expecting the inner CV joint to be shot and the cause of the problem, as this is what it now sounded like.
I rang the garage a few days later to check on progress, but was told having changed the complete driveshaft and CV joint assembly, the noise still persisted when decelerating, and would check the drivers side.
A couple of days later and I received a call to say the noise was still present having changed driveshafts and CV joints on both sides, and the problem is likely to be the gearbox.

The noise was present all the time when I last drove it, accelerating, deccelarating, coasting not so much but still there, and sounded exactly like CV joint noise. But now apparently only happening when slowing down (haven't driven it yet so can not confirm)

Has anyone else had this issue, is there something else that it could be.

Apologies for the essay!