I don't think it's ideal to run it with one flap missing, either have them all or remove all. That cylinder will be getting more or less air compared to other cylinders depending on rpm but the same amount of fuel as rest on that bank so could be running lean or rich and cause damage to the engine if too lean or cats and O2 sensors if too rich.
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Currently 8less
2011 Q7 S Line 3.0TDI, 2016 Tesla Model S 90D
8 history:
2006 A8 Sport 4.2TDI quattro SOLD,
1997 S8, reached end of life with gearbox failure
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