When you're seeking to know in how long from now someone will complete an activity, can you say "How long will you be?"
And what's your recommended phrase if this is incorrect?
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How long will you be?
The emphasis here is not on the task, but when the person (you) will be free. If somebody is working on a task that's nothing to do with you, but you want to know whether to wait for the person before, say, going for lunch, then this expression is perfect. You could also say
Will you be long?
If you want to ask how long it will take to complete a task that you have some interest in, you would be more likely to phrase the question to focus on the task (it), not the person, for example:
How long will it take?