Index: lucene/src/java/org/apache/lucene/index/DocumentsWriter.java
===================================================================
--- lucene/src/java/org/apache/lucene/index/DocumentsWriter.java	(revision 1149727)
+++ lucene/src/java/org/apache/lucene/index/DocumentsWriter.java	(working copy)
@@ -309,6 +309,9 @@
   }
 
   private boolean postUpdate(DocumentsWriterPerThread flushingDWPT, boolean maybeMerge) throws IOException {
+    if (flushControl.doApplyAllDeletes()) {
+      applyAllDeletes(deleteQueue);
+    }
     if (flushingDWPT != null) {
       maybeMerge |= doFlush(flushingDWPT);
     } else {
Index: lucene/src/java/org/apache/lucene/index/DocumentsWriterFlushControl.java
===================================================================
--- lucene/src/java/org/apache/lucene/index/DocumentsWriterFlushControl.java	(revision 1149727)
+++ lucene/src/java/org/apache/lucene/index/DocumentsWriterFlushControl.java	(working copy)
@@ -339,7 +339,11 @@
    * Returns the number of delete terms in the global pool
    */
   public int getNumGlobalTermDeletes() {
-    return documentsWriter.deleteQueue.numGlobalTermDeletes();
+    return documentsWriter.deleteQueue.numGlobalTermDeletes() + documentsWriter.indexWriter.bufferedDeletesStream.numTerms();
+  }
+  
+  public long getDeleteBytesUsed() {
+    return documentsWriter.deleteQueue.bytesUsed() + documentsWriter.indexWriter.bufferedDeletesStream.bytesUsed();
   }
 
   synchronized int numFlushingDWPT() {
Index: lucene/src/java/org/apache/lucene/index/FlushByRamOrCountsPolicy.java
===================================================================
--- lucene/src/java/org/apache/lucene/index/FlushByRamOrCountsPolicy.java	(revision 1149727)
+++ lucene/src/java/org/apache/lucene/index/FlushByRamOrCountsPolicy.java	(working copy)
@@ -65,7 +65,7 @@
     // prevent too-frequent flushing of a long tail of
     // tiny segments:
     if ((flushOnRAM() &&
-        writer.deleteQueue.bytesUsed() > (1024*1024*indexWriterConfig.getRAMBufferSizeMB()/2))) {
+        control.getDeleteBytesUsed() > (1024*1024*indexWriterConfig.getRAMBufferSizeMB()/2))) {
       control.setApplyAllDeletes();
      if (writer.infoStream != null) {
        writer.message("force apply deletes bytesUsed=" +  writer.deleteQueue.bytesUsed() + " vs ramBuffer=" + (1024*1024*indexWriterConfig.getRAMBufferSizeMB()));
Index: lucene/src/test/org/apache/lucene/index/TestIndexWriterDelete.java
===================================================================
--- lucene/src/test/org/apache/lucene/index/TestIndexWriterDelete.java	(revision 1149727)
+++ lucene/src/test/org/apache/lucene/index/TestIndexWriterDelete.java	(working copy)
@@ -944,4 +944,88 @@
     w.close();
     dir.close();
   }
+
+  // LUCENE-3340: make sure deletes that we don't apply
+  // during flush (ie are just pushed into the stream) are
+  // in fact later flushed due to their RAM usage:
+  public void testFlushPushedDeletesByRAM() throws Exception {
+    Directory dir = newDirectory();
+    // Cannot use RandomIndexWriter because we don't want to
+    // ever call commit() for this test:
+    IndexWriter w = new IndexWriter(dir,
+                                    newIndexWriterConfig(TEST_VERSION_CURRENT, new MockAnalyzer(random))
+                                    .setRAMBufferSizeMB(1.0f).setMaxBufferedDocs(1000).setMergePolicy(NoMergePolicy.NO_COMPOUND_FILES).setReaderPooling(false));
+    w.setInfoStream(VERBOSE ? System.out : null);
+    int count = 0;
+    while(true) {
+      Document doc = new Document();
+      doc.add(new Field("id", count+"", Field.Store.NO, Field.Index.NOT_ANALYZED));
+      final Term delTerm;
+      if (count == 1010) {
+        // This is the only delete that applies
+        delTerm = new Term("id", ""+0);
+      } else {
+        // These get buffered, taking up RAM, but delete
+        // nothing when applied:
+        delTerm = new Term("id", "x" + count);
+      }
+      w.updateDocument(delTerm, doc);
+      // Eventually segment 0 should get a del docs:
+      if (dir.fileExists("_0_1.del")) {
+        if (VERBOSE) {
+          System.out.println("TEST: deletes created @ count=" + count);
+        }
+        break;
+      }
+      count++;
+
+      // Today we applyDelets @ count=7199; even if we make
+      // sizable improvements to RAM efficiency of buffered
+      // del term we're unlikely to go over 100K:
+      if (count > 100000) {
+        fail("delete's were not applied");
+      }
+    }
+    w.close();
+    dir.close();
+  }
+
+  // LUCENE-3340: make sure deletes that we don't apply
+  // during flush (ie are just pushed into the stream) are
+  // in fact later flushed due to their RAM usage:
+  public void testFlushPushedDeletesByCount() throws Exception {
+    Directory dir = newDirectory();
+    // Cannot use RandomIndexWriter because we don't want to
+    // ever call commit() for this test:
+    final int flushAtDelCount = atLeast(1020);
+    IndexWriter w = new IndexWriter(dir,
+                                    newIndexWriterConfig(TEST_VERSION_CURRENT, new MockAnalyzer(random)).
+                                    setMaxBufferedDeleteTerms(flushAtDelCount).setMaxBufferedDocs(1000).setRAMBufferSizeMB(IndexWriterConfig.DISABLE_AUTO_FLUSH).setMergePolicy(NoMergePolicy.NO_COMPOUND_FILES).setReaderPooling(false));
+    w.setInfoStream(VERBOSE ? System.out : null);
+    int count = 0;
+    while(true) {
+      Document doc = new Document();
+      doc.add(new Field("id", count+"", Field.Store.NO, Field.Index.NOT_ANALYZED));
+      final Term delTerm;
+      if (count == 1010) {
+        // This is the only delete that applies
+        delTerm = new Term("id", ""+0);
+      } else {
+        // These get buffered, taking up RAM, but delete
+        // nothing when applied:
+        delTerm = new Term("id", "x" + count);
+      }
+      w.updateDocument(delTerm, doc);
+      // Eventually segment 0 should get a del docs:
+      if (dir.fileExists("_0_1.del")) {
+        break;
+      }
+      count++;
+      if (count > flushAtDelCount) {
+        fail("delete's were not applied at count=" + flushAtDelCount);
+      }
+    }
+    w.close();
+    dir.close();
+  }
 }