If you have the factory tools to work the ECU you dont need to disable anything. e.g. when installing new fuel injectors in a toyota D4S engine you need to enter the calibration numbers in it - what that does is make the ECU learn what is the new threshold for the new adaptation.
In similar context when repairing a proprietary transmission like an allison or a MB passenger or even heavy duty you need to put the new information in there otherwise the system shows you the finger and goes to sleep.
By tuning if you say you have turboed an NA engine and are going the ECU remap (hack) route its useless - I have been down that road more than a dozen times, the only way to make it YOUR SLAVE is to have a system that you write from scratch like a motec etc or you invent your own hardware (seen that a lot in EU to drive turboed mercedes benz)