Go to "Settings->Shortcut Mapper". From there, select the corresponding tab and right-click on the macro or run command. From there you can edit or remove said item. Selecting the item and then clicking the Modify or Delete button has the same respective effect. The Delete button is active on the Macro and Run tabs only, as well as the Delete entry on the right click menu.
Scintilla commands cannot be deleted, and can be bound to several key combinations. In the latter cases, simply select the target shortcut and choose Remove. If there is only one shortcut, select it, choose None as key (shifts won't matter) and click Apply. In either case, clicking Ok will remove the shortcut, while Cancel leaves it untouched.
The Macro -> Modify shortcvut / Delete macro and Run -> Modify shortcut / Delete command are handy shortcuts for the procedure described above.