I also deactivated the AGR (Abgasrückführung) on my Golf 4 AHF (81 kW). I did it initially just to test. After that, the car still drives exactly as well as before; the acceleration is good, at least. However, subjectively, the 'boost' that you usually feel with a TDI is missing. Either I didn't seal the vacuum hose properly, or the boost pressure is now built up more evenly, and the engine runs more smoothly.
I'll look into the issue with the flush calculation tool again.
What are your experiences with this? Perhaps even long-term experiences?