It will reset the app and will start without your personal data/settings.
When iGO starts up it will always create a save folder and in there it places the settings of the current state of your system, so each time you go into one of the settings and change something then it will update the save folder with those new changed settings.
The reason it's suggested to delete the save folder is just in case the settings or the sys.txt file saved in the save folder something it's messed up.
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