Index: lucene/CHANGES.txt
===================================================================
--- lucene/CHANGES.txt	(revision 1086202)
+++ lucene/CHANGES.txt	(working copy)
@@ -14,6 +14,12 @@
 * LUCENE-2990: ArrayUtil/CollectionUtil.*Sort() methods now exit early
   on empty or one-element lists/arrays.  (Uwe Schindler)
 
+Bug fixes
+
+* LUCENE-2996: addIndexes(IndexReader) did not flush before adding the new 
+  indexes, causing existing deletions to be applied on the incoming indexes as 
+  well. (Shai Erera)
+
 ======================= Lucene 3.1 (not yet released) =======================
 
 Changes in backwards compatibility policy
Index: lucene/src/test/org/apache/lucene/index/TestAddIndexes.java
===================================================================
--- lucene/src/test/org/apache/lucene/index/TestAddIndexes.java	(revision 1086202)
+++ lucene/src/test/org/apache/lucene/index/TestAddIndexes.java	(working copy)
@@ -911,5 +911,39 @@
     
     assertEquals("Only one compound segment should exist", 3, dir.listAll().length);
   }
+ 
+  // LUCENE-2996: tests that addIndexes(IndexReader) applies existing deletes correctly.
+  public void testExistingDeletes() throws Exception {
+    Directory[] dirs = new Directory[2];
+    for (int i = 0; i < dirs.length; i++) {
+      dirs[i] = newDirectory();
+      IndexWriterConfig conf = newIndexWriterConfig(TEST_VERSION_CURRENT, new MockAnalyzer());
+      IndexWriter writer = new IndexWriter(dirs[i], conf);
+      Document doc = new Document();
+      doc.add(new Field("id", "myid", Store.NO, Index.NOT_ANALYZED_NO_NORMS));
+      writer.addDocument(doc);
+      writer.close();
+    }
+
+    IndexWriterConfig conf = new IndexWriterConfig(TEST_VERSION_CURRENT, new MockAnalyzer());
+    IndexWriter writer = new IndexWriter(dirs[0], conf);
+
+    // Now delete the document
+    writer.deleteDocuments(new Term("id", "myid"));
+    IndexReader r = IndexReader.open(dirs[1]);
+    try {
+      writer.addIndexes(r);
+    } finally {
+      r.close();
+    }
+    writer.commit();
+    assertEquals("Documents from the incoming index should not have been deleted", 1, writer.numDocs());
+    writer.close();
+
+    for (Directory dir : dirs) {
+      dir.close();
+    }
+
+  }
   
 }
Index: lucene/src/java/org/apache/lucene/index/IndexWriter.java
===================================================================
--- lucene/src/java/org/apache/lucene/index/IndexWriter.java	(revision 1086202)
+++ lucene/src/java/org/apache/lucene/index/IndexWriter.java	(working copy)
@@ -2913,6 +2913,10 @@
     ensureOpen();
 
     try {
+      if (infoStream != null)
+        message("flush at addIndexes(IndexReader...)");
+      flush(false, true);
+
       String mergedName = newSegmentName();
       SegmentMerger merger = new SegmentMerger(directory, config.getTermIndexInterval(),
                                                mergedName, null, payloadProcessorProvider,