"...it may develop fault codes of bad sites left and bad sites right."
Well, this is certainly clear (not). What the heck is a bad site? Sounds like something you shouldn't point your browser to :-)
The ECU setups in our cars are predominently Closed Loop, which means the ECU sniffs the exhaust content via the Lambda (O2) Sensors and adjusts the fueling accordingly. This is called Fuel Trim and these trims are stored in various data Sites in the ECU's 3D map. All sites have a range of permitted values and if these are exceeded, then the Engine Light can be fired. There are plenty of OBD2 Error Codes out there that include the words "implausible value" or "out of range" and these show values measured that are out of range.
EU3 cars were actually setup fairly rich as far as I am aware, which meant that the fitting of a free flowing Stage-1 setup (from any source in truth) would normally have the required level of fueling available already, but if the Lambda's decided that they needed more (or less) fuel at any particular point, the ECU would 'trim' at that site. Too much trimming and a Check Engine light would fire.
So in my view an EU3 car should be fine without a re-flash of the ECU and even if it did fire a CEL, then a simple reset with ProTune would have you on your way again. A CEL caused by out-of-range fuel trims is unlikely to have any noticeable effect on how the car drives though.
