diff --git a/CHANGELOG.adoc b/CHANGELOG.adoc
index 268d6d14e8..ca1ac85ec7 100644
--- a/CHANGELOG.adoc
+++ b/CHANGELOG.adoc
@@ -10,6 +10,7 @@ Release with new features and bugfixes:
 * https://github.com/devonfw/IDEasy/issues/1006[#1006]: Eclipse automation opens UI that blocks further processing until closed
 * https://github.com/devonfw/IDEasy/issues/1110[#1110]: ide status fails with IllegalStateException when offline
 * https://github.com/devonfw/IDEasy/issues/1039[#1039]: Update Jasypt commandlet implementation to run Java version from dependencies.json
+* https://github.com/devonfw/IDEasy/issues/1138[#1138]: Duplicated variables in configuration logs a clear warning and do not prevent merge anymore
 
 The full list of changes for this release can be found in https://github.com/devonfw/IDEasy/milestone/24?closed=1[milestone 2025.03.002].
 
diff --git a/cli/src/main/java/com/devonfw/tools/ide/merge/xmlmerger/XmlMergeStrategy.java b/cli/src/main/java/com/devonfw/tools/ide/merge/xmlmerger/XmlMergeStrategy.java
index 3a878e1316..bc00646a7e 100644
--- a/cli/src/main/java/com/devonfw/tools/ide/merge/xmlmerger/XmlMergeStrategy.java
+++ b/cli/src/main/java/com/devonfw/tools/ide/merge/xmlmerger/XmlMergeStrategy.java
@@ -60,7 +60,6 @@ protected void doMerge(Element templateElement, Element resultElement, ElementMa
    * @param matcher the {@link ElementMatcher}.
    */
   public void merge(Element templateElement, Element resultElement, ElementMatcher matcher) {
-
     try {
       doMerge(templateElement, resultElement, matcher);
     } catch (XmlMergeException e) {
diff --git a/cli/src/main/java/com/devonfw/tools/ide/merge/xmlmerger/matcher/ElementMatcher.java b/cli/src/main/java/com/devonfw/tools/ide/merge/xmlmerger/matcher/ElementMatcher.java
index 1e069f4fb6..d39d09abc6 100644
--- a/cli/src/main/java/com/devonfw/tools/ide/merge/xmlmerger/matcher/ElementMatcher.java
+++ b/cli/src/main/java/com/devonfw/tools/ide/merge/xmlmerger/matcher/ElementMatcher.java
@@ -45,7 +45,7 @@ private IdComputer getIdComputer(Element element) {
     } else {
       this.qName2IdMap.putIfAbsent(qName, id);
     }
-    return this.id2ComputerMap.computeIfAbsent(id, IdComputer::new);
+    return this.id2ComputerMap.computeIfAbsent(id, i -> new IdComputer(i, context));
   }
 
   /**
diff --git a/cli/src/main/java/com/devonfw/tools/ide/merge/xmlmerger/matcher/IdComputer.java b/cli/src/main/java/com/devonfw/tools/ide/merge/xmlmerger/matcher/IdComputer.java
index d4c9ee7586..13d89f1798 100644
--- a/cli/src/main/java/com/devonfw/tools/ide/merge/xmlmerger/matcher/IdComputer.java
+++ b/cli/src/main/java/com/devonfw/tools/ide/merge/xmlmerger/matcher/IdComputer.java
@@ -9,6 +9,7 @@
 import org.w3c.dom.Element;
 import org.w3c.dom.NodeList;
 
+import com.devonfw.tools.ide.context.IdeContext;
 import com.devonfw.tools.ide.merge.xmlmerger.XmlMergeSupport;
 
 /**
@@ -19,17 +20,23 @@ public class IdComputer {
   /** The value of merge:id that is used to evaluate the xpath expression. */
   private final String id;
 
+  private final IdeContext context;
+
   private static final XPathFactory xPathFactory = XPathFactory.newInstance();
 
+  private final boolean throwExceptionOnMultipleMatches = Boolean.parseBoolean(System.getProperty("throwExceptionOnMultipleMatches", "false"));
+
+
   /**
    * The constructor.
    *
    * @param id the {@link #getId() merge ID}.
    */
-  public IdComputer(String id) {
+  public IdComputer(String id, IdeContext context) {
 
     super();
     this.id = id;
+    this.context = context;
   }
 
   /**
@@ -61,8 +68,14 @@ public Element evaluateExpression(Element templateElement, Element workspaceElem
       } else if (length == 0) {
         return null;
       } else {
-        throw new IllegalStateException(
-            length + " matches found for XPath " + xpathExpr + " in workspace XML at " + XmlMergeSupport.getXPath(workspaceElement, true));
+        if (throwExceptionOnMultipleMatches) {
+          throw new IllegalStateException(
+              length + " matches found for XPath " + xpathExpr + " in workspace XML at " + XmlMergeSupport.getXPath(workspaceElement, true));
+        } else {
+          this.context.warning("Matches found: {} matches for XPath {} in workspace XML at {}",
+              length, xpathExpr, XmlMergeSupport.getXPath(workspaceElement, true));
+        }
+        return (Element) nodeList.item(0);
       }
     } catch (XPathExpressionException e) {
       throw new IllegalStateException("Failed to compile XPath expression " + xpath, e);