Yes, you're right. You could interpret it as "from whom.." as in "who brought them" or maybe "who had them before", if that's what you mean by "from whom are those books". I think in that case, to make it clearer, we'd probably ask in a different way where it's more explicit. Something like:
¿Quién tenía esos libros?
¿A quién pertenecían esos libros?
Is this what you mean?
Or are you maybe referring to "who the author is"? In that case, that could be another interpretation if we say ¿De quienes son esos libros? (e.g "esos libros son todos de Cervantes")
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