Why is not Tom working today? I think it means that Tom is not working today, he has a day off, he is at home or somewhere else but he is not at his workplace. There is another situation. If I need Tom and I came at his workplace and I know he should be there but instead of him I see Boris. How should I ask "Why is Boris working today? why is not Tom working today?" Does it the same sentence with different meaning?
Why is Boris working in Tom's place today? Why has Boris taken Tom's job today? Why is Boris working Tom's job today?
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Why is Boris working in Tom's place today?
Why has Boris taken Tom's job today?
Why is Boris working Tom's job today?
pupilWhy is not Tom working today?
You have 'not' in the wrong place.
Why is Tom not working today?
CJ