make sure that the dealer updated the calibration in the ecm. sometimes these issues have calibration updates to prevent them from occurring but you don't about them unless someone checks the current calibration number in the ecm against the latest calibration on cummins quickserve. black smoke will not happen on engines with a dpf system unless there is severe damage to the DPF, the DOC is probably face plugged so bad it can't be cleaned, if there are fault codes for the turbo that could have cause or contributed to the problems, for things to get this bad there are most likely a long list of fault codes that have been ignored for a long time, all of this info is stored in the ecm and accessed with cummins insite diag tool that all cummins dealers have