Index: trunk/src/org/openstreetmap/josm/data/osm/DataSetMerger.java
===================================================================
--- trunk/src/org/openstreetmap/josm/data/osm/DataSetMerger.java	(revision 14916)
+++ trunk/src/org/openstreetmap/josm/data/osm/DataSetMerger.java	(revision 14922)
@@ -318,5 +318,5 @@
             //
         } else if (!target.isModified() && !source.isModified() && target.isVisible() != source.isVisible()
-                && target.getVersion() == source.getVersion())
+                && target.getVersion() == source.getVersion()) {
             // Same version, but different "visible" attribute and neither of them are modified.
             // It indicates a serious problem in datasets.
@@ -325,8 +325,12 @@
             throw new DataIntegrityProblemException(tr("Conflict in ''visible'' attribute for object of type {0} with id {1}",
                     target.getType(), target.getId()));
-        else if (target.isDeleted() && !source.isDeleted() && target.getVersion() == source.getVersion()) {
+        } else if (target.isDeleted() && !source.isDeleted() && target.getVersion() == source.getVersion()) {
             // same version, but target is deleted. Assume target takes precedence
             // otherwise too many conflicts when refreshing from the server
-            // but, if source has a referrer that is not in the target dataset there is a conflict
+            // but, if source is modified, there is a conflict
+            if (source.isModified()) {
+                addConflict(new Conflict<>(target, source, true));
+            }
+            // or, if source has a referrer that is not in the target dataset there is a conflict
             // If target dataset refers to the deleted primitive, conflict will be added in fixReferences method
             for (OsmPrimitive referrer: source.getReferrers()) {