Reversing a bad (non cummins) tune

[DVT873]

This is not a RED engine. It is an International medium-duty DT466. Bench flashed it back to stock and cust installed it. Unit starts runs and drives but has a power issue*. Only making about 17 #'s of boost. Some things are messed up beyond the reach of a factory reflash. I have the factory software, the International equivalent of Insite. Injector buzz test does not run. Had a CEL on but no codes. In the parameters, I had an error for the EBP sensor. Not the usual place to look. Sensor was unplugged. That should have set a standaed DTC. It did not. Plugged it back in error message went away, and the CEL went out.
In looking over the engine, the EGR valve and ITV were unplugged. Again there should have been normal DTC's. There weren't. Not even any error messages on the parameter screen like the EBP set. Several other standard tests that run from the diagnostic program don't run.

A bit of backstory. Truck ran fine after initial demandate. About 3 weeks in, this power problem popped up. There is another truck in the area, different owner, same issue. Same 3-week time frame. The same guy did both. So far, nobody has told me who he is, and I don't care. He tells them it can't be his tune. Whatever.

Today I got a call from a shop I do some work with. Same story, same engine, demandate, runs three weeks and then low power. I don't know if it is the same tuner.

New or rebuilt ECM is not available. I have a used one coming and will program it and see what happens.

Going back to my origional question, it looks to me that at least on these International ECMs there may be some programming that is hard coded to the ECM? For lack of a better term? Something that a normal reflash isn't getting to.