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My friend is Chinese and is learning English. In conversation she asked me which of these were correct:
'In three hours, I don't know what I should do'
or

'In three hours, I don't know what should I do'
She was asking me what she should do with herself for three hours while she waits for someone, so I think staright away she should substitute 'in' for 'for'.

Neither of them sound correct to me and embarrasingly I couldn't tell her which (if any) was correct. Could someone please check over them and;
a) tell me if either or indeed both are correct or not, and;
b) explain to me why they are correct/incorrect.
I have a feeling that the latter of the two would constitue informal, lazy grammar use in everyday speech but am not too sure?!?
Comments  
'In three hours, I don't know what should I do' incorrect grammar, unless there is a special reason within the style but it does not apply here

'In three hours, I don't know what I should do'
is correct but the meaning is

"After three hours pass, I don't know what I should do."

It sounds very strange to place "in (or for) three hours" at the beginning. It sounds better at the end of the sentence.

I don't know what I should do for three hours.

Should is not the best choice. Three hours is long time. The speaker cannot decide about his action or if there is an appropriate action at all. Should is used better if you have several options but you can't make a choice, or if you know you probably have an obligation but cannot recognize it at the moment.

I don't know what I'm going to do for three hours.
I don't know what I'm going to do for the next three hours.


is probably the most precise.
Hi pjyrdo
Here are my comments:
1. The word order is not the most natural. The time aspect is more typical at the end: "I don't know what I should do for three hours."

2. 'In three hours' is frequently used to refer to a point in time that is three hours from now. (e.g. I'll see you in three hours.) Your friend should use 'for' instead of 'in' because 'for' is typically used to talk about duration of time. Using 'in' will easily lead to misinterpretation. (e.g. "I don't know what I should do three hours from now.")

3. "I don't know what I should do" is correct. That is an indirect question. However, indirect questions generally do not use interrogative word order. The word order should be the same as in an affirmative sentence. Your friend should be able to find this in any grammar book.
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I have a feeling that the intent of the question is: I don't know what I should do between now and three hours from now, during the next three hours.
<<>> She was asking me what she should do with herself for three hours while she waits for someone. Scenario: she drove an hour to the airport to pick up someone and due to a snow storm, the arrival flight was hung up for 3 hours. She didn't want to drive home, only to come back a couple of hours later. Based on this context, the answer was already in the sentence, "with".
I don't know what I should do with the next 3 hours while waiting ...just my 2 cents.
BTW
Question from a non-native speaker that got stumped
Students: We have free audio pronunciation exercises.
Sorry for asking....should it be more appropriate with "who" got stumped ? I know "that" in some cases may work.
BTW I actually meant,
Question from a non-native speaker that stumped me.
NOT
Question from a non-native speaker that got stumped.

I left out the article and the pronoun for brevity.
Thanks for your input. Most helpful