diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/AdditionalInput.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/AdditionalInput.java
index ed49c353ccf..43bbc228fd5 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/AdditionalInput.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/AdditionalInput.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2005, 2016 Intel Corporation and others.
+ * Copyright (c) 2005, 2019 Intel Corporation and others.
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
  * which accompanies this distribution, and is available at
@@ -9,6 +9,7 @@
  *     Intel Corporation - Initial API and implementation
  *     IBM Corporation
  *     Marc-Andre Laperle
+ *     EclipseSource
  *******************************************************************************/
 package org.eclipse.cdt.managedbuilder.internal.core;
 
@@ -128,6 +129,10 @@ public class AdditionalInput implements IAdditionalInput {
 	 * @param additionalInput The existing AdditionalInput to clone.
 	 */
 	public AdditionalInput(IInputType parent, AdditionalInput additionalInput) {
+		this(parent, additionalInput, false);
+	}
+
+	public AdditionalInput(IInputType parent, AdditionalInput additionalInput, boolean retainRebuildState) {
 		this.fParent = parent;
 		fIsExtensionAdditionalInput = false;
 
@@ -140,8 +145,13 @@ public class AdditionalInput implements IAdditionalInput {
 			fKind = additionalInput.fKind;
 		}
 
-		setDirty(true);
-		setRebuildState(true);
+		if (retainRebuildState) {
+			setDirty(additionalInput.fIsDirty);
+			setRebuildState(additionalInput.fRebuildState);
+		} else {
+			setDirty(true);
+			setRebuildState(true);
+		}
 	}
 
 	/*
diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/InputOrder.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/InputOrder.java
index c2de80fc8cc..bf1a2e49889 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/InputOrder.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/InputOrder.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2005, 2016 Intel Corporation and others.
+ * Copyright (c) 2005, 2019 Intel Corporation and others.
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
  * which accompanies this distribution, and is available at
@@ -8,6 +8,7 @@
  * Contributors:
  * Intel Corporation - Initial API and implementation
  * IBM Corporation
+ * EclipseSource
  *******************************************************************************/
 package org.eclipse.cdt.managedbuilder.internal.core;
 
@@ -90,6 +91,17 @@ public class InputOrder implements IInputOrder {
 	 * @param inputOrder The existing InputOrder to clone.
 	 */
 	public InputOrder(IInputType parent, InputOrder inputOrder) {
+		this(parent, inputOrder, false);
+	}
+
+	/**
+	 * Create an <code>InputOrder</code> based upon an existing InputOrder.
+	 *
+	 * @param parent The <code>IInputType</code> the InputOrder will be added to.
+	 * @param inputOrder The existing InputOrder to clone.
+	 * @param retainRebuildState Whether or not to retain the <code>rebuildState</code> and <code>dirty</code> state of <code>inputOrder</code>.
+	 */
+	public InputOrder(IInputType parent, InputOrder inputOrder, boolean retainRebuildState) {
 		this.fParent = parent;
 		fIsExtensionInputOrder = false;
 
@@ -106,8 +118,13 @@ public class InputOrder implements IInputOrder {
 			fExcluded = inputOrder.fExcluded;
 		}
 
-		setDirty(true);
-		setRebuildState(true);
+		if (retainRebuildState) {
+			setDirty(inputOrder.fIsDirty);
+			setRebuildState(inputOrder.fRebuildState);
+		} else {
+			setDirty(true);
+			setRebuildState(true);
+		}
 	}
 
 	/*
diff --git a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/InputType.java b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/InputType.java
index 67529585dc1..6ae00f3b06c 100644
--- a/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/InputType.java
+++ b/build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/InputType.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2005, 2016 Intel Corporation and others.
+ * Copyright (c) 2005, 2019 Intel Corporation and others.
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
  * which accompanies this distribution, and is available at
@@ -8,6 +8,7 @@
  * Contributors:
  * Intel Corporation - Initial API and implementation
  * IBM Corporation
+ * EclipseSource
  *******************************************************************************/
 package org.eclipse.cdt.managedbuilder.internal.core;
 
@@ -229,7 +230,7 @@ public class InputType extends BuildObject implements IInputType {
 		if (inputType.sourceContentTypeIds != null) {
 			sourceContentTypeIds = inputType.sourceContentTypeIds.clone();
 		}
-		if(inputType.sourceContentTypes != null) {
+		if (inputType.sourceContentTypes != null) {
 			sourceContentTypes = inputType.sourceContentTypes.clone();
 		}
 		if (inputType.inputExtensions != null) {
@@ -279,18 +280,18 @@ public class InputType extends BuildObject implements IInputType {
 		//  Clone the children
 		if (inputType.inputOrderList != null) {
 			for (InputOrder inputOrder : inputType.getInputOrderList()) {
-				InputOrder newInputOrder = new InputOrder(this, inputOrder);
+				InputOrder newInputOrder = new InputOrder(this, inputOrder, copyIds);
 				getInputOrderList().add(newInputOrder);
 			}
 		}
 		if (inputType.additionalInputList != null) {
 			for (AdditionalInput additionalInput : inputType.getAdditionalInputList()) {
-				AdditionalInput newAdditionalInput = new AdditionalInput(this, additionalInput);
+				AdditionalInput newAdditionalInput = new AdditionalInput(this, additionalInput, copyIds);
 				getAdditionalInputList().add(newAdditionalInput);
 			}
 		}
 
-		if (copyIds){
+		if (copyIds) {
 			isDirty = inputType.isDirty;
 			rebuildState = inputType.rebuildState;
 		} else {