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Flight Mode Switch setup:
The recommended setup for running AutoTune uses a 3 position Flight Mode Switch.  With this, you can fly Attitude with default PIDs, AutoTune with default PIDs and Attitude with new PIDs, all without using the GCS:
Pos#1 - Attitude mode using bank 1
Pos#2 - AutoTune using bank 1 with SystemIdentSystemIdentSettings.DestinationPidBank set to 2 (that is the default)
Pos#3 - Attitude mode using bank 2 (bank 2 is where the tuned PIDs are written by default)
You also must enable the AutoTune module in GCS -> System -> Settings -> HwSettings -> OptionalModules -> AutoTune -> "set to Enabled", highlight OptionalModules by clicking on it, and press the red up arrow at the top of the screen to save it permanently.  This setup can all be done at home, and everything else can be done at the flying field, without using the GCS. 

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