Is it possible the variable turbo vanes are sticking, which gives an overboost condition and could be putting the ECU into limp-home mode? This happens with the VW 1.9 TDI and is accompanied by a sudden loss of power after driving with high boost.
If so, there are various turbo cleaning products available like Revive or Innotec which might be worth a try, though since they need to be fed directly into the turbo it's probably a garage job.
First off, you could check the variable vane actuator arm on the side of the turbo is free to move by hand (it's a metal rod which actuates a short metal arm via a pivot) and if it seems rough or sticky then I guess you might have a problem.
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