At the moment, there is only a single set of Menu Shortcut Settings which apply to both the Project and VI windows. The settings should be completely independent for each window, which would allow (a) the same keyboard shortcut to be used for two different functions in each window, and (b) disabling or changing the shortcut for only one of the windows.
I started this idea from wanting to disable Ctrl-E in the Project window -- with a large project, switching to the File view can hang LabVIEW for some minutes. But I can't do that without also disabling it in the VI window, and I use that a lot. Which also explains why I get sick of doing it when I don't realise a Project window is actually topmost.
The Ctrl-E part of this idea is also noted in this declined idea.
Any idea that has not received any kudos within a year after posting will be automatically declined.