I tried reproducing this using MP 1.3.70 and writing about 20 of the ATC_xxx parameters, then disconnected and reconnected the USB cable (to reboot the board) but again, no issues.
Do you think you could come up with a list of detailed steps to reproduce the issue? It may depend upon which version of ArduPilot and MP are being used so if you can tell me that as well that would be great. For example, in my test I used MP 1.3.70 build 1.3.7353.42041 and the vehicle had ArduCopter V4.0.3-rc1.
Ideally if you have an onboard log file from before and then another from after it has been reset to defaults that would be fantastic. It may be necessary to set LOG_DISARMED = 1 in order to create a log while the vehicle is disarmed.