When the engine/aircraft combination is certified, there are 'factors' applied to address normal engine to engine variability (often referred to as 'minimum engine'), and the aircraft power setting charts take into account thrust uncertainties due to external effects (humidity is a big one at higher temps - high humidity reduces the air density which in turn reduces thrust at N1). As a general rule, there is less variability in thrust at EPR than for thrust at N1, so N1 engines end up with larger 'min engine' factors (it's also why, when operating an EPR in alternate N1 mode, you may have a performance penalty).
All that being said, there are cases where engines start moving outside the 'normal' variability range. That happened a while back on the PW2000 - it was discovered that the way the leading edge of the fan blades abraded on high time engines caused a significant loss of thrust at EPR. As a result, a performance penalty had to be applied until the fan blades could be re-profiled to regain the original performance.