Logs of actual and requested boost, along with wastegate valve duty cycle and intake airflow (g/s) would help narrow down if issue is on ECU/control side or if problem is mechanical. Also try logging the knock sensor signal voltages, could be that ECU is pulling back boost due to something like knock sensor input (bad tank of low octane gas?, clogged intercooler?).
I know on later B8 2.0 Audis with IHI turbo, a P0299 code is pretty common when the wastegate flapper valve wears out prematurely and develops loose play in the swingarm linkage connection and shaft; allowing exhaust pressure to escape through wastegate before onset of boost. If you had a boost leak somewhere in the pressure side pipes or intercooler plumbing, you would probably see high airflow measurements at the AFM (upstream of turbo), without accompanying boost pressure. However, it does not make much sense that a mechanical problem would be intermittent.
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