1. A method of reconciling a first data structure with a second data structure, comprising: creating a first copy and a second copy of at least a portion of an original version of the first data structure; modifying the second copy in a document analysis process to create the second data structure; receiving at least a portion of a second version of the first data structure; mapping each node in the second data structure to a corresponding node in the first copy; analyzing each node in the at least a portion of the second version of the first data structure to determine if the node includes changes from a corresponding node in the first copy; and if an analyzed node includes changes from a corresponding node in the first copy, adding the corresponding node to a list of nodes for which changes will not be propagated to the first data structure.