Index: CHANGES.txt
===================================================================
--- CHANGES.txt	(revision 890721)
+++ CHANGES.txt	(working copy)
@@ -53,6 +53,9 @@
 
 * LUCENE-2142: FieldCacheImpl.getStringIndex no longer throws an
   exception when term count exceeds doc count.  (Mike McCandless)
+
+* LUCENE-2158: At high indexing rates, NRT reader could temporarily
+  lose deletions.  (Mike McCandless)
   
 New features
 
Index: src/test/org/apache/lucene/index/TestIndexWriterReader.java
===================================================================
--- src/test/org/apache/lucene/index/TestIndexWriterReader.java	(revision 890721)
+++ src/test/org/apache/lucene/index/TestIndexWriterReader.java	(working copy)
@@ -866,4 +866,34 @@
     r.close();
     dir.close();
   }
+
+  public void testDeletesNumDocs() throws Throwable {
+    Directory dir = new MockRAMDirectory();
+    final IndexWriter w = new IndexWriter(dir, new WhitespaceAnalyzer(),
+                                               IndexWriter.MaxFieldLength.LIMITED);
+    Document doc = new Document();
+    doc.add(new Field("field", "a b c", Field.Store.NO, Field.Index.ANALYZED));
+    Field id = new Field("id", "", Field.Store.NO, Field.Index.NOT_ANALYZED);
+    doc.add(id);
+    id.setValue("0");
+    w.addDocument(doc);
+    id.setValue("1");
+    w.addDocument(doc);
+    IndexReader r = w.getReader();
+    assertEquals(2, r.numDocs());
+    r.close();
+
+    w.deleteDocuments(new Term("id", "0"));
+    r = w.getReader();
+    assertEquals(1, r.numDocs());
+    r.close();
+
+    w.deleteDocuments(new Term("id", "1"));
+    r = w.getReader();
+    assertEquals(0, r.numDocs());
+    r.close();
+
+    w.close();
+    dir.close();
+  }
 }
Index: src/java/org/apache/lucene/index/IndexWriter.java
===================================================================
--- src/java/org/apache/lucene/index/IndexWriter.java	(revision 890721)
+++ src/java/org/apache/lucene/index/IndexWriter.java	(working copy)
@@ -395,12 +395,13 @@
     // this method is called:
     poolReaders = true;
 
-    flush(true, true, true);
+    flush(true, true, false);
     
     // Prevent segmentInfos from changing while opening the
     // reader; in theory we could do similar retry logic,
     // just like we do when loading segments_N
     synchronized(this) {
+      applyDeletes();
       return new ReadOnlyDirectoryReader(this, segmentInfos, termInfosIndexDivisor);
     }
   }
@@ -3654,7 +3655,6 @@
       }
 
       if (flushDeletes) {
-        flushDeletesCount++;
         applyDeletes();
       }
       
@@ -4423,6 +4423,7 @@
   // Apply buffered deletes to all segments.
   private final synchronized boolean applyDeletes() throws CorruptIndexException, IOException {
     assert testPoint("startApplyDeletes");
+    flushDeletesCount++;
     SegmentInfos rollback = (SegmentInfos) segmentInfos.clone();
     boolean success = false;
     boolean changed;