Index: lucene/CHANGES.txt
===================================================================
--- lucene/CHANGES.txt	(revision 1525890)
+++ lucene/CHANGES.txt	(working copy)
@@ -85,6 +85,10 @@
 * LUCENE-4998: Fixed a few places to pass IOContext.READONCE instead
   of IOContext.READ (Shikhar Bhushan via Mike McCandless)
 
+* LUCENE-5242: DirectoryTaxonomyWriter.replaceTaxonomy did not fully reset
+  its state, which could result in exceptions being thrown, as well as
+  incorrect ordinals returned from getParent. (Shai Erera)
+
 API Changes:
 
 * LUCENE-5222: Add SortField.needsScores(). Previously it was not possible
Index: lucene/facet/src/java/org/apache/lucene/facet/taxonomy/directory/DirectoryTaxonomyWriter.java
===================================================================
--- lucene/facet/src/java/org/apache/lucene/facet/taxonomy/directory/DirectoryTaxonomyWriter.java	(revision 1525890)
+++ lucene/facet/src/java/org/apache/lucene/facet/taxonomy/directory/DirectoryTaxonomyWriter.java	(working copy)
@@ -981,6 +981,7 @@
     initReaderManager(); // ensure that it's initialized
     refreshReaderManager();
     nextID = indexWriter.maxDoc();
+    taxoArrays = null; // must nullify so that it's re-computed next time it's needed
     
     // need to clear the cache, so that addCategory won't accidentally return
     // old categories that are in the cache.
@@ -987,6 +988,7 @@
     cache.clear();
     cacheIsComplete = false;
     shouldFillCache = true;
+    cacheMisses.set(0);
     
     // update indexEpoch as a taxonomy replace is just like it has be recreated
     ++indexEpoch;
Index: lucene/facet/src/test/org/apache/lucene/facet/taxonomy/directory/TestDirectoryTaxonomyWriter.java
===================================================================
--- lucene/facet/src/test/org/apache/lucene/facet/taxonomy/directory/TestDirectoryTaxonomyWriter.java	(revision 1525890)
+++ lucene/facet/src/test/org/apache/lucene/facet/taxonomy/directory/TestDirectoryTaxonomyWriter.java	(working copy)
@@ -469,4 +469,27 @@
     
     IOUtils.close(indexDir, taxoDir);
   }
+  
+  @Test
+  public void testReplaceTaxoWithLargeTaxonomy() throws Exception {
+    Directory srcTaxoDir = newDirectory(), targetTaxoDir = newDirectory();
+    
+    // build source, large, taxonomy
+    DirectoryTaxonomyWriter taxoWriter = new DirectoryTaxonomyWriter(srcTaxoDir);
+    int ord = taxoWriter.addCategory(new CategoryPath("A/1/1/1/1/1/1", '/'));
+    taxoWriter.close();
+    
+    taxoWriter = new DirectoryTaxonomyWriter(targetTaxoDir);
+    int ordinal = taxoWriter.addCategory(new CategoryPath("B/1", '/'));
+    assertEquals(1, taxoWriter.getParent(ordinal)); // call getParent to initialize taxoArrays
+    taxoWriter.commit();
+    
+    taxoWriter.replaceTaxonomy(srcTaxoDir);
+    assertEquals(ord - 1, taxoWriter.getParent(ord));
+    taxoWriter.close();
+    
+    srcTaxoDir.close();
+    targetTaxoDir.close();
+  }
+  
 }