I have seen both versions in use, like “What do you have in/on mind?” Are the two prepositions here totally interchangeable?
They are not interchangeable.
What do you have in mind? - Means what are you thinking about doing (regarding something undefined here)?
What do you have on your mind? - Means what are you thinking about?
What do you have on mind? - is incorrect.
So, when I’d like to ask “What do you mean?”, which one of those would fit better?
Neither would work if you wish to ask ‘what do you mean?’