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?
_________________
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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Canadian-American native speaker
who teaches English for a living at Mister Micawber's
ESL cafe: Interview with Mister Micawber

[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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_________________
Amy
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ESL teacher, and native speaker of American English

[Mister Micawber]

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But you were more lucid, Yank.
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_________________
Canadian-American native speaker
who teaches English for a living at Mister Micawber's
ESL cafe: Interview with Mister Micawber