Index: src/test/org/apache/lucene/index/TestIndexWriterReader.java
===================================================================
--- src/test/org/apache/lucene/index/TestIndexWriterReader.java	(revision 786154)
+++ src/test/org/apache/lucene/index/TestIndexWriterReader.java	(working copy)
@@ -805,4 +805,29 @@
     r.close();
     dir1.close();
   }
+
+  public void testExpungeDeletes() 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);
+    w.deleteDocuments(new Term("id", "0"));
+
+    IndexReader r = w.getReader();
+    w.expungeDeletes();
+    w.close();
+    r.close();
+    r = IndexReader.open(dir);
+    assertEquals(1, r.numDocs());
+    assertFalse(r.hasDeletions());
+    r.close();
+    dir.close();
+  }
 }
Index: src/java/org/apache/lucene/index/LogMergePolicy.java
===================================================================
--- src/java/org/apache/lucene/index/LogMergePolicy.java	(revision 786154)
+++ src/java/org/apache/lucene/index/LogMergePolicy.java	(working copy)
@@ -303,7 +303,16 @@
     int firstSegmentWithDeletions = -1;
     for(int i=0;i<numSegments;i++) {
       final SegmentInfo info = segmentInfos.info(i);
-      if (info.hasDeletions()) {
+      boolean deletionsInRAM = false;
+      SegmentReader sr = writer.readerPool.getIfExists(info);
+      try {
+        deletionsInRAM = sr != null && sr.hasDeletions();
+      } finally {
+        if (sr != null) {
+          writer.readerPool.release(sr);
+        }
+      }
+      if (info.hasDeletions() || deletionsInRAM) {
         if (verbose())
           message("  segment " + info.name + " has deletions");
         if (firstSegmentWithDeletions == -1)
Index: src/java/org/apache/lucene/index/IndexWriter.java
===================================================================
--- src/java/org/apache/lucene/index/IndexWriter.java	(revision 786154)
+++ src/java/org/apache/lucene/index/IndexWriter.java	(working copy)
@@ -625,6 +625,15 @@
       sr.incRef();
       return sr;
     }
+
+    // Returns a ref
+    public synchronized SegmentReader getIfExists(SegmentInfo info) throws IOException {
+      SegmentReader sr = (SegmentReader) readerMap.get(info);
+      if (sr != null) {
+        sr.incRef();
+      }
+      return sr;
+    }
   }
   
   synchronized void acquireWrite() {
@@ -4142,19 +4151,11 @@
 
       docWriter.pushDeletes();
 
-      if (flushDocs)
+      if (flushDocs) {
         segmentInfos.add(newSegment);
-
-      if (flushDeletes) {
-        flushDeletesCount++;
-        applyDeletes();
+        checkpoint();
       }
-      
-      doAfterFlush();
 
-      if (flushDocs)
-        checkpoint();
-
       if (flushDocs && mergePolicy.useCompoundFile(segmentInfos, newSegment)) {
         // Now build compound file
         boolean success = false;
@@ -4173,6 +4174,16 @@
         checkpoint();
       }
 
+      if (flushDeletes) {
+        flushDeletesCount++;
+        applyDeletes();
+      }
+      
+      if (flushDocs)
+        checkpoint();
+
+      doAfterFlush();
+
       return flushDocs;
 
     } catch (OutOfMemoryError oom) {