What do people mean when they say
How do you mean?
Are they asking me to explain what I just said? Then how is it different from
What do you mean?
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What do you mean? is commonly known and usually said when one does not comprehend what the other said. Basically it is asking for a repeat of the sentence in more detail.
How do you mean? is a little different. How can be defined as in what way or manner.
How does this work?
In what way or manner does this work?
Both sentences are basically the same. So, How do you mean? is asking:
In what way or manner do you mean?