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In XML Data Integration, data/metadata merging and query processing are indispensable. Specifically, merging integrates multiple disparate (heterogeneous and autonomous) input data sources together for further usage, while query processing is one main reason why the data need to be integrated in the first place. Besides, when supported with appropriate user feedback techniques, queries can also provide contexts in which conflicts among the input sources can be interpreted and resolved. The flexibility of XML structure provides opportunities for alleviating some of the difficulties that other less flexible data types face in the presence of uncertainty; yet, this flexibility also introduces new challenges in merging multiple sources and query processing over integrated data. In this chapter, the authors discuss two alternative ways XML data/schema can be integrated: conflict-eliminating (where the result is cleaned from any conflicts that the different sources might have with each other) and conflict-preserving (where the resulting XML data or XML schema captures the alternative interpretations of the data). They also present techniques for query processing over integrated, possibly imprecise, XML data, and cover strategies that can be used for resolving underlying conflicts.