Isn't the LML the one that's prone to ghost code on delete tunes? I remember reading about it when tuning was new for the LML. Something to do with an unrelated code needing to be disabled that fixed the issue. And not all trucks suffered from the issue. Always results in a limp mode with no codes or DIC warnings.
I think there was two ways to get it out of limp, reflash the ECM, even flashing the same tune will work, or adjusting the offending code and flashing that tune in
It seems like this may be a possibility