diff --git a/ome-xml/src/test/java/ome/xml/utests/ReferenceIndexingTest.java b/ome-xml/src/test/java/ome/xml/utests/ReferenceIndexingTest.java
new file mode 100644
index 000000000..5b2c15754
--- /dev/null
+++ b/ome-xml/src/test/java/ome/xml/utests/ReferenceIndexingTest.java
@@ -0,0 +1,259 @@
+/*
+ * #%L
+ * OME XML library
+ * %%
+ * Copyright (C) 2006 - 2016 Open Microscopy Environment:
+ *   - Massachusetts Institute of Technology
+ *   - National Institutes of Health
+ *   - University of Dundee
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package ome.xml.utests;
+
+import static org.testng.AssertJUnit.*;
+
+import ome.xml.meta.MetadataConverter;
+import ome.xml.meta.OMEXMLMetadataImpl;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+/**
+ * Tests for indexed reference handling in OMEXMLMetadataImpl.
+ *
+ * These tests verify that references can be appended sequentially and
+ * replaced at specific indices without causing NullPointerException.
+ */
+public class ReferenceIndexingTest {
+
+  private OMEXMLMetadataImpl meta;
+
+  @BeforeMethod
+  public void setUp() {
+    meta = new OMEXMLMetadataImpl();
+  }
+
+  /**
+   * Test sequential appending of ROI references to an Image.
+   * This tests the fix for the NPE when calling linkROI(null).
+   */
+  @Test
+  public void testAppendImageROIReferences() {
+    // Set up Image and ROIs
+    meta.setImageID("Image:0", 0);
+    meta.setROIID("ROI:0", 0);
+    meta.setROIID("ROI:1", 1);
+    meta.setROIID("ROI:2", 2);
+
+    // Append ROI references sequentially
+    meta.setImageROIRef("ROI:0", 0, 0);
+    meta.setImageROIRef("ROI:1", 0, 1);
+    meta.setImageROIRef("ROI:2", 0, 2);
+
+    // Verify count
+    assertEquals(3, meta.getImageROIRefCount(0));
+
+    // Verify each reference
+    assertEquals("ROI:0", meta.getImageROIRef(0, 0));
+    assertEquals("ROI:1", meta.getImageROIRef(0, 1));
+    assertEquals("ROI:2", meta.getImageROIRef(0, 2));
+  }
+
+  /**
+   * Test replacement of ROI references at specific indices.
+   */
+  @Test
+  public void testReplaceImageROIReferences() {
+    // Set up Image and ROIs
+    meta.setImageID("Image:0", 0);
+    meta.setROIID("ROI:0", 0);
+    meta.setROIID("ROI:1", 1);
+    meta.setROIID("ROI:2", 2);
+    meta.setROIID("ROI:3", 3);
+
+    // Append ROI references
+    meta.setImageROIRef("ROI:0", 0, 0);
+    meta.setImageROIRef("ROI:1", 0, 1);
+    meta.setImageROIRef("ROI:2", 0, 2);
+
+    assertEquals(3, meta.getImageROIRefCount(0));
+
+    // Replace middle reference
+    meta.setImageROIRef("ROI:3", 0, 1);
+
+    // Verify count unchanged
+    assertEquals(3, meta.getImageROIRefCount(0));
+
+    // Verify replacement
+    assertEquals("ROI:0", meta.getImageROIRef(0, 0));
+    assertEquals("ROI:3", meta.getImageROIRef(0, 1));
+    assertEquals("ROI:2", meta.getImageROIRef(0, 2));
+  }
+
+  /**
+   * Test that references survive MetadataConverter conversion.
+   */
+  @Test
+  public void testROIReferencesAfterConversion() {
+    // Set up source metadata
+    meta.setImageID("Image:0", 0);
+    meta.setROIID("ROI:0", 0);
+    meta.setROIID("ROI:1", 1);
+    meta.setImageROIRef("ROI:0", 0, 0);
+    meta.setImageROIRef("ROI:1", 0, 1);
+
+    assertEquals(2, meta.getImageROIRefCount(0));
+
+    // Convert to new metadata store
+    OMEXMLMetadataImpl out = new OMEXMLMetadataImpl();
+    MetadataConverter.convertMetadata(meta, out);
+
+    // Verify references survived conversion
+    assertEquals(2, out.getImageROIRefCount(0));
+    assertEquals("ROI:0", out.getImageROIRef(0, 0));
+    assertEquals("ROI:1", out.getImageROIRef(0, 1));
+  }
+
+  /**
+   * Test sequential appending of Annotation references to an Image.
+   */
+  @Test
+  public void testAppendImageAnnotationReferences() {
+    // Set up Image and Annotations
+    meta.setImageID("Image:0", 0);
+    meta.setCommentAnnotationID("Annotation:0", 0);
+    meta.setCommentAnnotationID("Annotation:1", 1);
+    meta.setCommentAnnotationID("Annotation:2", 2);
+
+    // Append annotation references sequentially
+    meta.setImageAnnotationRef("Annotation:0", 0, 0);
+    meta.setImageAnnotationRef("Annotation:1", 0, 1);
+    meta.setImageAnnotationRef("Annotation:2", 0, 2);
+
+    // Verify count
+    assertEquals(3, meta.getImageAnnotationRefCount(0));
+
+    // Verify each reference
+    assertEquals("Annotation:0", meta.getImageAnnotationRef(0, 0));
+    assertEquals("Annotation:1", meta.getImageAnnotationRef(0, 1));
+    assertEquals("Annotation:2", meta.getImageAnnotationRef(0, 2));
+  }
+
+  /**
+   * Test replacement of Annotation references at specific indices.
+   */
+  @Test
+  public void testReplaceImageAnnotationReferences() {
+    // Set up Image and Annotations
+    meta.setImageID("Image:0", 0);
+    meta.setCommentAnnotationID("Annotation:0", 0);
+    meta.setCommentAnnotationID("Annotation:1", 1);
+    meta.setCommentAnnotationID("Annotation:2", 2);
+    meta.setCommentAnnotationID("Annotation:3", 3);
+
+    // Append annotation references
+    meta.setImageAnnotationRef("Annotation:0", 0, 0);
+    meta.setImageAnnotationRef("Annotation:1", 0, 1);
+    meta.setImageAnnotationRef("Annotation:2", 0, 2);
+
+    assertEquals(3, meta.getImageAnnotationRefCount(0));
+
+    // Replace first reference
+    meta.setImageAnnotationRef("Annotation:3", 0, 0);
+
+    // Verify count unchanged
+    assertEquals(3, meta.getImageAnnotationRefCount(0));
+
+    // Verify replacement
+    assertEquals("Annotation:3", meta.getImageAnnotationRef(0, 0));
+    assertEquals("Annotation:1", meta.getImageAnnotationRef(0, 1));
+    assertEquals("Annotation:2", meta.getImageAnnotationRef(0, 2));
+  }
+
+  /**
+   * Test multiple images with ROI references.
+   */
+  @Test
+  public void testMultipleImagesWithROIReferences() {
+    // Set up multiple Images and ROIs
+    meta.setImageID("Image:0", 0);
+    meta.setImageID("Image:1", 1);
+    meta.setROIID("ROI:0", 0);
+    meta.setROIID("ROI:1", 1);
+    meta.setROIID("ROI:2", 2);
+
+    // Add ROIs to first image
+    meta.setImageROIRef("ROI:0", 0, 0);
+    meta.setImageROIRef("ROI:1", 0, 1);
+
+    // Add ROIs to second image
+    meta.setImageROIRef("ROI:1", 1, 0);
+    meta.setImageROIRef("ROI:2", 1, 1);
+
+    // Verify counts
+    assertEquals(2, meta.getImageROIRefCount(0));
+    assertEquals(2, meta.getImageROIRefCount(1));
+
+    // Verify first image references
+    assertEquals("ROI:0", meta.getImageROIRef(0, 0));
+    assertEquals("ROI:1", meta.getImageROIRef(0, 1));
+
+    // Verify second image references
+    assertEquals("ROI:1", meta.getImageROIRef(1, 0));
+    assertEquals("ROI:2", meta.getImageROIRef(1, 1));
+  }
+
+  /**
+   * Test append and replace in same sequence.
+   */
+  @Test
+  public void testMixedAppendAndReplace() {
+    meta.setImageID("Image:0", 0);
+    meta.setROIID("ROI:0", 0);
+    meta.setROIID("ROI:1", 1);
+    meta.setROIID("ROI:2", 2);
+    meta.setROIID("ROI:3", 3);
+
+    // Append first two
+    meta.setImageROIRef("ROI:0", 0, 0);
+    meta.setImageROIRef("ROI:1", 0, 1);
+    assertEquals(2, meta.getImageROIRefCount(0));
+
+    // Replace first
+    meta.setImageROIRef("ROI:2", 0, 0);
+    assertEquals(2, meta.getImageROIRefCount(0));
+
+    // Append third
+    meta.setImageROIRef("ROI:3", 0, 2);
+    assertEquals(3, meta.getImageROIRefCount(0));
+
+    // Verify final state
+    assertEquals("ROI:2", meta.getImageROIRef(0, 0));
+    assertEquals("ROI:1", meta.getImageROIRef(0, 1));
+    assertEquals("ROI:3", meta.getImageROIRef(0, 2));
+  }
+}
diff --git a/xsd-fu/templates/java/OMEXMLMetadataImpl.template b/xsd-fu/templates/java/OMEXMLMetadataImpl.template
index 561ac5ec7..8798a3665 100644
--- a/xsd-fu/templates/java/OMEXMLMetadataImpl.template
+++ b/xsd-fu/templates/java/OMEXMLMetadataImpl.template
@@ -137,10 +137,38 @@
     // ${prop.name} is reference and occurs more than once
     ${prop.name} ${prop.instanceVariableName}_reference = new ${prop.name}();
     ${prop.instanceVariableName}_reference.setID(${prop.argumentName});
+{% if prop.maxOccurs > 1 %}\
+    // Try to resolve reference immediately if the referenced object exists
+    OMEModelObject referencedObj = model.getModelObject(${prop.argumentName});
+    if (referencedObj != null && referencedObj instanceof ${prop.langType})
+    {
+      ${prop.langType} typedRef = (${prop.langType}) referencedObj;
+      ${obj.langType} concreteObject = ${join_accessors(obj.name, parent, prop)};
+      // Extend list by one element if needed (only allows sequential growth)
+      if (concreteObject.sizeOfLinked${prop.methodName}List() == ${index_name_string(prop.name)})
+      {
+        concreteObject.link${prop.methodName}(typedRef);
+      }
+      else
+      {
+        // Set at specific index
+        concreteObject.setLinked${prop.methodName}(${index_name_string(prop.name)}, typedRef);
+      }
+    }
+    else
+    {
+      // Deferred resolution: reference will be resolved later
+      model.addReference(
+        ${join_accessors(obj.name, parent, prop)},
+        ${prop.instanceVariableName}_reference);
+    }
+{% end %}\
+{% if prop.maxOccurs == 1 %}\
     model.addReference(
       ${join_accessors(obj.name, parent, prop)},
       ${prop.instanceVariableName}_reference);
 {% end %}\
+{% end %}\
 {% otherwise %}\
     // ${prop.name} is not a reference
     OME o0 = root;