Index: /src/org/openstreetmap/josm/data/osm/visitor/MergeVisitor.java
===================================================================
--- /src/org/openstreetmap/josm/data/osm/visitor/MergeVisitor.java	(revision 56)
+++ /src/org/openstreetmap/josm/data/osm/visitor/MergeVisitor.java	(revision 57)
@@ -1,5 +1,8 @@
 package org.openstreetmap.josm.data.osm.visitor;
 
+import java.util.HashMap;
 import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.Map;
 
 import org.openstreetmap.josm.data.osm.DataSet;
@@ -20,4 +23,17 @@
 	private final DataSet ds;
 	
+	/**
+	 * A list of all nodes that got replaced with other nodes.
+	 * Key is the node in the other's dataset and the value is the one that is now
+	 * in ds.nodes instead.
+	 */
+	private final Map<Node, Node> mergedNodes = new HashMap<Node, Node>();
+	/**
+	 * A list of all line segments that got replaced with others.
+	 * Key is the segment in the other's dataset and the value is the one that is now
+	 * in ds.lineSegments.
+	 */
+	private final Map<LineSegment, LineSegment> mergedLineSegments = new HashMap<LineSegment, LineSegment>();
+	
 	public MergeVisitor(DataSet ds) {
 		this.ds = ds;
@@ -39,4 +55,5 @@
 			ds.nodes.add(otherNode);
 		else {
+			mergedNodes.put(otherNode, myNode);
 			mergeCommon(myNode, otherNode);
 			if (myNode.modified && !otherNode.modified)
@@ -64,4 +81,5 @@
 			ds.lineSegments.add(otherLs);
 		else {
+			mergedLineSegments.put(otherLs, myLs);
 			mergeCommon(myLs, otherLs);
 			if (myLs.modified && !otherLs.modified)
@@ -99,7 +117,6 @@
 			Iterator<LineSegment> it = otherTrack.segments.iterator();
 			for (LineSegment ls : myTrack.segments) {
-				if (!match(ls, it.next())) {
+				if (!match(ls, it.next()))
 					same = false;
-				}
 			}
 			if (!same) {
@@ -113,4 +130,37 @@
 	public void visit(Key k) {
 		//TODO: Key doesn't really fit the OsmPrimitive concept!
+	}
+	
+	/**
+	 * Postprocess the dataset and fix all merged references to point to the actual
+	 * data.
+	 */
+	public void fixReferences() {
+		for (LineSegment ls : ds.lineSegments) {
+			if (mergedNodes.containsKey(ls.start))
+				ls.start = mergedNodes.get(ls.start);
+			if (mergedNodes.containsKey(ls.end))
+				ls.end = mergedNodes.get(ls.end);
+		}
+		for (Track t : ds.tracks) {
+			boolean replacedSomething = false;
+			LinkedList<LineSegment> newSegments = new LinkedList<LineSegment>();
+			for (LineSegment ls : t.segments) {
+				LineSegment otherLs = mergedLineSegments.get(ls);
+				newSegments.add(otherLs == null ? ls : otherLs);
+				if (otherLs != null)
+					replacedSomething = true;
+			}
+			if (replacedSomething) {
+				t.segments.clear();
+				t.segments.addAll(newSegments);
+			}
+			for (LineSegment ls : t.segments) {
+				if (mergedNodes.containsKey(ls.start))
+					ls.start = mergedNodes.get(ls.start);
+				if (mergedNodes.containsKey(ls.end))
+					ls.end = mergedNodes.get(ls.end);
+			}
+		}
 	}
 	
Index: /src/org/openstreetmap/josm/gui/layer/OsmDataLayer.java
===================================================================
--- /src/org/openstreetmap/josm/gui/layer/OsmDataLayer.java	(revision 56)
+++ /src/org/openstreetmap/josm/gui/layer/OsmDataLayer.java	(revision 57)
@@ -136,4 +136,5 @@
 		for (OsmPrimitive osm : ((OsmDataLayer)from).data.allPrimitives())
 			osm.visit(visitor);
+		visitor.fixReferences();
 	}
 
Index: /test/org/openstreetmap/josm/test/MergeVisitorTest.java
===================================================================
--- /test/org/openstreetmap/josm/test/MergeVisitorTest.java	(revision 56)
+++ /test/org/openstreetmap/josm/test/MergeVisitorTest.java	(revision 57)
@@ -7,5 +7,7 @@
 import org.openstreetmap.josm.data.osm.LineSegment;
 import org.openstreetmap.josm.data.osm.Node;
+import org.openstreetmap.josm.data.osm.OsmPrimitive;
 import org.openstreetmap.josm.data.osm.visitor.MergeVisitor;
+import org.openstreetmap.josm.test.framework.Bug;
 import org.openstreetmap.josm.test.framework.DataSetTestCaseHelper;
 
@@ -19,14 +21,11 @@
 	public void testMergeOldLineSegmentsWithNew() {
 		DataSet ds = new DataSet();
-		Node n1 = DataSetTestCaseHelper.createNode(ds);
-		n1.id = 1;
-		Node n2 = DataSetTestCaseHelper.createNode(ds);
-		n2.id = 2;
-		LineSegment ls1 = DataSetTestCaseHelper.createLineSegment(ds, n1, n2);
+		Node[] n = createNodes(ds, 2);
+		LineSegment ls1 = DataSetTestCaseHelper.createLineSegment(ds, n[0], n[1]);
 		ls1.id = 3;
 
 		Node newnode = new Node();
-		newnode.coor = new GeoPoint(n2.coor.lat, n2.coor.lon);
-		LineSegment newls = new LineSegment(n1, newnode);
+		newnode.coor = new GeoPoint(n[1].coor.lat, n[1].coor.lon);
+		LineSegment newls = new LineSegment(n[0], newnode);
 
 		MergeVisitor v = new MergeVisitor(ds);
@@ -34,3 +33,44 @@
 		assertEquals("line segment should have been merged.", 1, ds.lineSegments.size());
 	}
+	
+	/**
+	 * Nodes beeing merged are equal but not the same.
+	 */
+	@Bug(54)
+	public void testEqualNotSame() {
+		// create a dataset with line segment a-b
+		DataSet ds = new DataSet();
+		Node n[] = createNodes(ds, 2);
+		LineSegment ls1 = DataSetTestCaseHelper.createLineSegment(ds, n[0], n[1]);
+		ls1.id = 1;
+		
+		// create an other dataset with line segment a'-c (a' is equal, but not same to a)
+		DataSet ds2 = new DataSet();
+		Node n2[] = createNodes(ds2, 2);
+		n2[0].coor = new GeoPoint(n[0].coor.lat, n[0].coor.lon);
+		n2[1].id = 42;
+		LineSegment ls2 = DataSetTestCaseHelper.createLineSegment(ds, n2[0], n2[1]);
+		
+		MergeVisitor v = new MergeVisitor(ds);
+		for (OsmPrimitive osm : ds2.allPrimitives())
+			osm.visit(v);
+		v.fixReferences();
+		
+		assertSame(ls1.start, ls2.start);
+	}
+	
+	
+	/**
+	 * Create that amount of nodes and add them to the dataset. The id will be 1,2,3,4...
+	 * @param amount Number of nodes to create.
+	 * @return The created nodes.
+	 */
+	private Node[] createNodes(DataSet ds, int amount) {
+		Node[] nodes = new Node[amount];
+		for (int i = 0; i < amount; ++i) {
+			nodes[i] = DataSetTestCaseHelper.createNode(ds);
+			nodes[i].id = i+1;
+		}
+		return nodes;
+	}
 }