This issue arose in a recent lesson. In short, it centres on the difference between:
Where do you live?
I live in Tokyo. v In Tokyo. v Tokyo.
Which city do you live in?
I live in Tokyo? v ?In Tokyo. v Tokyo.
The issue is the answer 'In Tokyo', to the question 'Which city do you live in?'. There's no doubt about what it means, but my native speaker intuition says it's either not right or awkward (specifically, the 'in'), but in class I couldn't think of any reason why, and I haven't been able to find anything either way since. I can't recall hearing or reading it, and I wouldn't say or write it myself.
The issue isn't ending a question with a preposition. I would have the same issue with 'In which city do you live?' 'In Tokyo'. It also isn't with the preposition 'in'. I would have the same issue with 'Who did you vote for?' 'For Smith'.
So, is 'In Tokyo' a grammatical/acceptable response to 'Which city do you live in?'/'In which city do you live?'. Either way, is there an authoritative reference?