Well, at first they said they suspected it was the mechatronics and/or flywheel, they agreed to contribute 33% towards the final bill. But when the gearbox was out, they said the flywheel was ok and didn't need replacing. They just changed the mechatronics unit, I paid £980.10.
Drove away and the clunk noise was still there in 2nd and 4th so took it straight back. They took readings etc from ECU and gearbox and sent it to VW, they come back saying the car had been tampered with etc and that the map was causing the issue. I told them the map is not currently on the car and hasn't been for the past few months (and the new mechs wiped the DSG map anyway), in the end they decided it was the clutch packs. I asked if they would put my old mechs unit back in and reimburse me as that was not the cause of the issue, they insisted there was actually a fault with my mechs unit so would've needed replacing, I don't know if I believe that TBH but not worth the hassle trying to argue that... I had to pay for the parts but not the labour, worked out about another £320.