1. A method of reconciling results of ink analysis of a document with a current version of the document, the method comprising: creating document independent context object from a current context object of the document; creating a copy of the document independent context object; modifying the copy of the document independent context object in a document analysis process to include results of ink analysis of the document independent context object; receiving a second version of the current context object; for every ink node in the document independent context object, when there is a corresponding node in the current context object, then adding the node to a hash table which maps unique node identifiers in the document independent context object to node references in the current context object; for each node in the document independent context object, determining if the corresponding node in the second version of the current context object differs from the each node; and for each node in the document independent context object, when a node in the document independent context object differs from the corresponding node in the second version of the current context object, adding the node to a list of nodes for which changes will not be propagated.