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You can use ЛИ in three places of senstenses У НЕГО ЕСТЬ УЧЕБНИК?
1. Есть ли у него учебник? (question about ixisting of his textbook)

2. У него ли учебник? (question about place)...

1. у него есть учебник?
2. у него ли учебник?

In my opinion (native Russian speaker) this is two different sentences.
In 1. you ask: Has he a textbook? indeed. You don't know: is there a...