Like Simon mentioned you might want to create a document identifier or
UUID - if you don't have one already
and use this code snippet to check if doc exists:

 string doc_id = "1234567";
 Term idTerm = new Term(Fields.DOCID_FIELD,doc_id);
            if (mSearcher.docFreq(idTerm) > 0) {
                //mIndexWriter.updateDocument(idTerm,doc);
                //This document exists hence skip
            } else {
                mIndexWriter.addDocument(doc);
            }

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