Solutions
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coloneldolomite's post in Gearbox noise 1.6TDI was marked as the answerFinally the saga has been sorted out!
Even after fitting the new differential, the noise was apparently still there. In the end Skoda agreed to fitting a new gearbox to the car, which I wanted all along, so I am happy. It has amazed me the lengths the dealer had to go to before they would authorise this, in terms of labour time alone.
The noise has gone, so I can now get back on with enjoying the car again. Hopefully no more issues!