Index: /trunk/src/org/openstreetmap/josm/data/osm/DataSetMerger.java
===================================================================
--- /trunk/src/org/openstreetmap/josm/data/osm/DataSetMerger.java	(revision 3964)
+++ /trunk/src/org/openstreetmap/josm/data/osm/DataSetMerger.java	(revision 3965)
@@ -309,6 +309,7 @@
             // take. We take target.
             //
-        } else if (target.isVisible() != source.isVisible() && target.getVersion() == source.getVersion())
-            // Same version, but different "visible" attribute. It indicates a serious problem in datasets.
+        } else if (!target.isModified() && !source.isModified() && target.isVisible() != source.isVisible() && target.getVersion() == source.getVersion())
+            // Same version, but different "visible" attribute and neither of them are modified.
+            // It indicates a serious problem in datasets.
             // For example, datasets can be fetched from different OSM servers or badly hand-modified.
             // We shouldn't merge that datasets.
Index: /trunk/src/org/openstreetmap/josm/gui/layer/OsmDataLayer.java
===================================================================
--- /trunk/src/org/openstreetmap/josm/gui/layer/OsmDataLayer.java	(revision 3964)
+++ /trunk/src/org/openstreetmap/josm/gui/layer/OsmDataLayer.java	(revision 3965)
@@ -47,4 +47,5 @@
 import org.openstreetmap.josm.data.gpx.ImmutableGpxTrack;
 import org.openstreetmap.josm.data.gpx.WayPoint;
+import org.openstreetmap.josm.data.osm.DataIntegrityProblemException;
 import org.openstreetmap.josm.data.osm.DataSet;
 import org.openstreetmap.josm.data.osm.DataSetMerger;
@@ -65,6 +66,6 @@
 import org.openstreetmap.josm.data.validation.TestError;
 import org.openstreetmap.josm.gui.HelpAwareOptionPane;
+import org.openstreetmap.josm.gui.HelpAwareOptionPane.ButtonSpec;
 import org.openstreetmap.josm.gui.MapView;
-import org.openstreetmap.josm.gui.HelpAwareOptionPane.ButtonSpec;
 import org.openstreetmap.josm.gui.dialogs.LayerListDialog;
 import org.openstreetmap.josm.gui.dialogs.LayerListPopup;
@@ -299,5 +300,16 @@
     public void mergeFrom(final DataSet from) {
         final DataSetMerger visitor = new DataSetMerger(data,from);
-        visitor.merge();
+        try {
+            visitor.merge();
+        } catch (DataIntegrityProblemException e) {
+            JOptionPane.showMessageDialog(
+                    Main.parent,
+                    e.getMessage(),
+                    tr("Error"),
+                    JOptionPane.ERROR_MESSAGE
+            );
+            return;
+
+        }
 
         Area a = data.getDataSourceArea();