When the car arrives to yourself in limp mode with DPF light ON, the ecu has already disabled cruise control automatically, as cruise control can only be set if all functions in the ecu are working.

So the fix is, first off, the DPF needs to be regenerated and/or ash counter reset to restore Cruise Control and Gear Shift lights before reading the ECU. Once it is restored, the boot read can be taken, and the mod file applied, and cruise control will be active still. 

It is not possible to restore cruise control functions with the mod file loaded on.