There is a standard SAE pid for the number of key cycles/ignition cycles since the last module reset. An ECU reset will occur following an ECU flash (like an install/change map/uninstall with the Accessport), but also through disconnecting the battery terminals for a few minutes or using a handheld code reader to reset the ECU. In most cases, this pid will be what dealership technicians will reference when asking about whether or not the vehicle has been tuned if and when the number is 'suspiciously' low given mileage or age. As in cdurbin's experience above, this pid does not store any information about what sort of device commanded the reset. This is not to say that Ford - or any other modern OE manufacturer - lacks the capability to detect a previously installed tune, but in our experience the first check for a tune is done through this pid.
Booth9999 - Should you have problems like this in the future, please don't hesitate to reach out to us on the forums or through our customer service department. We are here to help and hopefully save unnecessary trips to the dealership and/or dollars spent. Also, to answer your earlier question, we do not clear as-built data from any module under any conditions.