Permant dtc's and no start on E38

I know exactly how the permanent dtc's work and how you need to do a universal drive cycle, but what happens if for example a car comes in with no rear o2s and the fuel control moduals been replace with a full fuel system? If the codes weren't turned off prior to the work then they are always stored as permanent codes even if the lights off. Thats not a huge deal though, its when someone sees them on a code scan and tries to do a code clear and after that the codes will still obviously be logged as a permanent still but the actual car goes into some limp mode where it will start up and stall after 2seconds. Usually you reflash the same tune back in and its fine till someone unknowingly clears it again. Is there anyway around this? Obviously you can't fix the problems and do a drive cycle???

*This is E38 platform btw.