The construction I want to form is
...which X to Verb "its" Noun.
Specifically this question: "How can I decide which book to read fully and which one to read only its summary?"
Is this question construction correct?
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The form you have proposed is not correct and not idiomatic in English. To express the idea behind it, you can say:
"How can I decide which book to read fully, and which to read [only] a summary of?"
Another possibility is: "How can I decide which book to read fully, and which book to read only as a summary."