Index: /trunk/src/org/openstreetmap/josm/actions/MergeLayerAction.java
===================================================================
--- /trunk/src/org/openstreetmap/josm/actions/MergeLayerAction.java	(revision 11122)
+++ /trunk/src/org/openstreetmap/josm/actions/MergeLayerAction.java	(revision 11123)
@@ -47,5 +47,6 @@
                         if (sourceLayer instanceof OsmDataLayer && targetLayer instanceof OsmDataLayer
                                 && ((OsmDataLayer) sourceLayer).isUploadDiscouraged() != ((OsmDataLayer) targetLayer).isUploadDiscouraged()) {
-                            if (warnMergingUploadDiscouragedLayers(sourceLayer, targetLayer)) {
+                            if (Boolean.TRUE.equals(GuiHelper.runInEDTAndWaitAndReturn(() ->
+                                    warnMergingUploadDiscouragedLayers(sourceLayer, targetLayer)))) {
                                 break;
                             }