segment swap???

Hello everyone, here is a beginner question because I don't know any better. I have a neighbor with a 2001 6.0L and a 4L60e in a Jeep, another tuner has been working on this and now I have the software and he is wanting me to tune for him. There is a driveability concern when transitioning from open loop to closed loop (cuts out, acts like there is no fuel) this can last from 10 seconds to a minute. Talking to the guy tuning, it doesn't sound like he has done the segment swap, only tried to use a 5.3/4L60 file and overwrite the 5.3 files with 6.0 files. The trans is working, so I assume he has rewired the connector at the trans. Can this be done without doing the segment swap. Sorry for the book, but would like to be educated before diving in and spending more of the customer money.