Query-based explanations for missing answers identify which operators of a query are responsible for the failure to return a missing answer of interest. This type of explanations has proven to be useful in a variety of contexts including debugging of complex analytical queries. Such queries are frequent in big data systems such as Apache Spark. We present a novel approach for producing query-based explanations. Our approach is the first to support nested data and to consider operators that modify the schema and structure of the data (e.g., nesting and projections) as potential causes of missing answers. To efficiently compute explanations, we propose a heuristic algorithm that applies two novel techniques: (i) reasoning about multiple schema alternatives for a query and (ii) re-validating at each step whether an intermediate result can contribute to the missing answer. Using an implementation of our approach on Spark, we demonstrate that it is the first to scale to large datasets and that it often finds explanations that existing techniques fail to identify.