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“So you can do what with it?” (The Postmistress by Sarah Blake, p.118)

And the focus of your research right now, Charles, is what? (Woman’s Hour, Mon, 28 Apr 14, 14'18")

Can above questions, not having subject-auxiliary inversion, be used as the same meaning as their normal syntactic forms: “So what can you do with it?”, “And what is the focus of your research right now, Charles?”

I find no differences between the two forms above, yet I’ve only read in CGEL that those types have some epistemic bias towards a positive or negative answer. Or they are used when what you heard is not clear or surprising (p,881;p.886). The questions above are or can be just simple, unbiased, questions or not?

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I don't think either of the specific questions you give as examples has a bias towards either a positive or negative answer, because neither can be answered with a simple positive or negative—they’re both ‘open-ended’ questions, conditioned by the what at the end of each. They can be spoken with varying emphasis and intonation, which may commit the speaker to a specific attitude. But that commitment is not a function of the syntactic form; the same attitude may be conveyed by emphasis and intonation in ordinary interrogatives

These, however, may indicate an ‘expected’ answer:

You can ask questions like this?
The focus of your research is English interrogatives?

These may express dismay, or excitement, or skepticism or confusion about the addressee's prior assertion of these propositions. And in fact, at least to my mind, what distinguishes questions of this sort from ordinary interrogatives with Subj/Aux inversion is that they are almost always responsive. That is, these questions are not used to initiate a discourse or to introduce a wholly new topic; they have to pick up on something that occurred earlier in the present discourse. Note that each of your examples opens with a conjunction, implying a continuation of something previous. My two examples likewise imply an established topic:

[So you are telling me] you can ask questions like this?
[Do you really think that] you can ask questions like this?

[I didn’t quite catch that …] the focus of your research is English interrogatives?
[You say that] the focus of your research is English interrogatives? [You’re not interested in French interrogatives?]

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Yes, there is a difference in emphasis.

What can you do with it?

is a simple, open-ended question.

You can do what with it?

has a skeptical implication. If I showed you my awesome new slide rule, and you said:

What are you going to do with it?

you might be honestly asking for information; you might be enthusiastic, you might be confused. But if you asked:

And you're going to do what with that, exactly?

it would be rude; the clear implication is that you think that it is a useless item and probably a waste of money. "Exactly" is commonly used to emphasize the negative implications of this kind of sentence.

Your second example:

And the focus of your research is what?

does not have as clear a negative implication; here, this would most likely be used when asking for clarification. You would never approach someone for the first time and say:

The focus of your research is what?

It's not by accident that the sentence you quote starts with "and"; this type of sentence almost always needs some kind of antecedent. What that antecedent is will determine the sense.

In summary: If you use it in context, the context determines the additional meaning, which is often a request for clarification or a negative implication.

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There seems to be some bias, although it is hard to tell without further context...

So you can do what with it?

It seems that the real question is not "what can you do with it?" but really "does it have any use?"

And the focus of your research right now, Charles, is what?

I can read this in two ways. If the speaker is introducing Charles to the audience, having explained that he is doing interesting research, the question may be simply the end of the introduction and a bridge for Charles to start speaking. Charles is likely to respond, to the speaker and then the audience, along these lines:

Thank you miss Johnson. I am currently focussing on...

However, if the speaker directly asks this of Charles, especially with a stress on what:

And the focus of your research right now, Charles, is what?

There could very well be a negative bias. The speaker does not at all seem convinced that Charles' research is interesting at all.

Alternatively, a subject came up that is very closely related to Charles current focus, and the speaker employs sarcasm to draw attention to the fact that the subject that came up should be of interest to Charles, but he doesn't seem to notice that.

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