"What is in the box?"
Translation:Wat zit er in de doos?
Thanks, Iwaka. Unfortunately, I don't remember what the other sentence I saw this pattern in was, so I can't really compare them now. I am pretty sure, though, that it also had the verb zitten and the in at the end, otherwise I don't think I would have tried my variant in the first place. So my question still remains, but it can be paraphrased: Is there such a verb as zitten but with the detachable prefix in? Or alternately, is there some other possible construction with in at the end?
In wat zit er in de doos? the preposition in is the Head of the prepositional phrase in de doos, so it cannot be placed anywhere else.
That being said, it is true that the verb inzitten exists, but it means something else ('worry'). This verb is indeed a separable verb, but you cannot use it here.
Hope this helps!