I am afraid that you have to do it manfully.
Go to your prefs folder. You can delete or rename this folder, but this action will reset all you Maya settings.
If you just want to reset Hypershade, find the file called "userPrefs.mel". In this file, search "// Hypershade". You can delete all this section for Hypershade. Or you can just delete this particular attribute:
-sv "hyperShadeDockingLayout" "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"