X15 with a Non-VGT turbo

[Dr watson]

One of my customers previously had his original isx engine engine deregulated and had since gone through 3 turbos. He had a catastrophic failure in cylinder #3 and had me do an engine swap. We installed an X15, but he is still using the reprogrammed ecm from the ISX. I was able to make it work after re-pinning a couple of pins to make it communicate. He also had me install a non-VGT turbo at the same time. He has probably put about 20k mi since the swap, {has a} CEL for the turbo Comm, but I'm concerned the ISX ecm may cause long term damage due to the different fueling rates. I need some help to reprogram his X15 ecm that came with his new engine to match his current vehicle configuration. Please, any guidance would be greatly appreciated.