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This question is very similar to Delete Global Hotkey however requires a different solution.

I know which application created the global hotkey. This application does not have any settings which allow me to disable or change the hotkeys (unlike the above question).

It is also really useful so I don't want to disable it, however it's getting in the way of working with other applications.

Is there a way I can force the global hotkey to be disabled? Preferably all hotkeys by this application.

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Until the Application is running the hotkey registered by it will be active. Either kill it from Task Manager when not needed or Locate Settings/Preferences in the application to change the Hotkey to some non used combination. – Ankit Mishra Jul 7 '13 at 6:16
@Lamb: He already said there are no such app settings. – Karan Jul 7 '13 at 23:28
@Annan: Do you want to use the same hotkey in other apps? Or simply disable the hotkey so that no app can use it? – Karan Jul 7 '13 at 23:31
@Karan I need to use the hotkey in other apps as a local hotkey. This is my main reason for wanting to disable the global version. – Annan Jul 8 '13 at 4:19
AutoHotkey can disable a global hotkey or an app's local hotkey, but I'm not sure it can disable one app's global hotkey so that the same can be used by another app as a local hotkey. Perhaps you can play around with it and see if it's possible. – Karan Jul 8 '13 at 16:24

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