Ken is mostly right. If you've manually set the shortcut keys, whichever workbook's got set first wins; even if you close all workbooks then open wb2 then wb1, wb1 will trump wb2 even if opened second.
However, having said that, you could always utilize the workbook's Activate() event handler to clear any assignments for the key and then assign your. For example, let's say your hotkey was Ctrl+m. You could do like so:
Code:
'// code module for workbook two
Private Sub Workbook_Activate()
With Application
.OnKey "^m"
.OnKey "^m", "MacroForWorkbookOne"
End With
End Sub
Code:
'// code module for workbook two
Private Sub Workbook_Activate()
With Application
.OnKey "^m"
.OnKey "^m", "MacroForWorkbookTwo"
End With
End Sub