Index: src/test/org/apache/lucene/index/TestIndexReader.java
===================================================================
--- src/test/org/apache/lucene/index/TestIndexReader.java	(revision 777080)
+++ src/test/org/apache/lucene/index/TestIndexReader.java	(working copy)
@@ -1590,6 +1590,27 @@
     IndexReader.open(dir).close();
   }
 
+  // LUCENE-1647
+  public void testIndexReaderUnDeleteAll() throws Exception {
+    MockRAMDirectory dir = new MockRAMDirectory();
+    dir.setPreventDoubleWrite(false);
+    IndexWriter writer = new IndexWriter(dir, new StandardAnalyzer(),
+                                         IndexWriter.MaxFieldLength.UNLIMITED);
+    writer.addDocument(createDocument("a"));
+    writer.addDocument(createDocument("b"));
+    writer.addDocument(createDocument("c"));
+    writer.close();
+    IndexReader reader = IndexReader.open(dir);
+    reader.deleteDocuments(new Term("id", "a"));
+    reader.flush();
+    reader.deleteDocuments(new Term("id", "b"));
+    reader.undeleteAll();
+    reader.deleteDocuments(new Term("id", "b"));
+    reader.close();
+    IndexReader.open(dir).close();
+    dir.close();
+  }
+
   private Document createDocument(String id) {
     Document doc = new Document();
     doc.add(new Field("id", id, Field.Store.YES, Field.Index.NOT_ANALYZED_NO_NORMS));
Index: src/test/org/apache/lucene/store/MockRAMDirectory.java
===================================================================
--- src/test/org/apache/lucene/store/MockRAMDirectory.java	(revision 777080)
+++ src/test/org/apache/lucene/store/MockRAMDirectory.java	(working copy)
@@ -215,7 +215,7 @@
     createdFiles.add(name);
     RAMFile existing = (RAMFile)fileMap.get(name);
     // Enforce write once:
-    if (existing!=null && !name.equals("segments.gen"))
+    if (existing!=null && !name.equals("segments.gen") && preventDoubleWrite)
       throw new IOException("file " + name + " already exists");
     else {
       if (existing!=null) {
Index: src/java/org/apache/lucene/index/SegmentReader.java
===================================================================
--- src/java/org/apache/lucene/index/SegmentReader.java	(revision 777080)
+++ src/java/org/apache/lucene/index/SegmentReader.java	(working copy)
@@ -57,12 +57,10 @@
   Ref deletedDocsRef = null;
   private boolean deletedDocsDirty = false;
   private boolean normsDirty = false;
-  private boolean undeleteAll = false;
   private int pendingDeleteCount;
 
   private boolean rollbackDeletedDocsDirty = false;
   private boolean rollbackNormsDirty = false;
-  private boolean rollbackUndeleteAll = false;
   private int rollbackPendingDeleteCount;
   IndexInput freqStream;
   IndexInput proxStream;
@@ -683,14 +681,14 @@
       clone.readBufferSize = readBufferSize;
       clone.cfsReader = cfsReader;
       clone.storeCFSReader = storeCFSReader;
-
+      
       clone.fieldInfos = fieldInfos;
       clone.tis = tis;
       clone.freqStream = freqStream;
       clone.proxStream = proxStream;
       clone.termVectorsReaderOrig = termVectorsReaderOrig;
       clone.fieldsReaderOrig = fieldsReaderOrig;
-      
+
       if (!openReadOnly && hasChanges) {
         // My pending changes transfer to the new reader
         clone.pendingDeleteCount = pendingDeleteCount;
@@ -762,11 +760,10 @@
       si.setDelCount(si.getDelCount()+pendingDeleteCount);
       pendingDeleteCount = 0;
       assert deletedDocs.count() == si.getDelCount(): "delete count mismatch during commit: info=" + si.getDelCount() + " vs BitVector=" + deletedDocs.count();
+    } else {
+      assert pendingDeleteCount == 0;
     }
-    if (undeleteAll && si.hasDeletions()) {
-      si.clearDelGen();
-      si.setDelCount(0);
-    }
+
     if (normsDirty) {               // re-write norms
       si.setNumFields(fieldInfos.size());
       Iterator it = norms.values().iterator();
@@ -779,7 +776,6 @@
     }
     deletedDocsDirty = false;
     normsDirty = false;
-    undeleteAll = false;
   }
 
   FieldsReader getFieldsReader() {
@@ -865,21 +861,23 @@
       oldRef.decRef();
     }
     deletedDocsDirty = true;
-    undeleteAll = false;
     if (!deletedDocs.getAndSet(docNum))
       pendingDeleteCount++;
   }
 
   protected void doUndeleteAll() {
     deletedDocsDirty = false;
-    undeleteAll = true;
     if (deletedDocs != null) {
       assert deletedDocsRef != null;
       deletedDocsRef.decRef();
       deletedDocs = null;
       deletedDocsRef = null;
+      pendingDeleteCount = 0;
+      si.clearDelGen();
+      si.setDelCount(0);
     } else {
       assert deletedDocsRef == null;
+      assert pendingDeleteCount == 0;
     }
   }
 
@@ -1254,7 +1252,6 @@
     super.startCommit();
     rollbackDeletedDocsDirty = deletedDocsDirty;
     rollbackNormsDirty = normsDirty;
-    rollbackUndeleteAll = undeleteAll;
     rollbackPendingDeleteCount = pendingDeleteCount;
     Iterator it = norms.values().iterator();
     while (it.hasNext()) {
@@ -1267,7 +1264,6 @@
     super.rollbackCommit();
     deletedDocsDirty = rollbackDeletedDocsDirty;
     normsDirty = rollbackNormsDirty;
-    undeleteAll = rollbackUndeleteAll;
     pendingDeleteCount = rollbackPendingDeleteCount;
     Iterator it = norms.values().iterator();
     while (it.hasNext()) {