Does this conversation sound natural?

[Daemon99]

Can someone please tell me if the following conversation sounds natural?

John: I have to make two folders and put all the modified files in one folder and the ones that were not modfied in the other.
Jake: How would you know what are modified and what are not?
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Non-native speaker of English
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I intend to live forever - so far, so good.

[Mister Micawber]

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John: I have to make two folders and put all the modified files in one folder and the ones that were not modified in the other.

Jake: How will you know which are modified and which are not?
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Native English teacher at Mister Micawber's

[Yankee]

Hi Daemon

I would prefer the word 'which' (instead of 'what') in your second sentence.

In addition, using the word 'would' suggests to me that Jake thinks John will have some trouble distinguishing between the two types. If you used 'will' instead of 'would', it would be a more straightforward question (i.e. no suggestion of presupposition).

That's my two cents.

EDIT:
Oops, I see MM was faster than I was.
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[Mister Micawber]

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But you were more lucid, Yank.
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Native English teacher at Mister Micawber's