Thank you kindly, Tiffany for a patch that helps:

Drag copy a prim and the prim that is moved, persists. 
The prim that is created does not survive a restart.

OpenSim/Region/Environment/Scenes/InnerScene.cs

@@ -1417,6 +1417,13 @@ namespace OpenSim.Region.Environment.Scenes
                         Entities.Add(copy.UUID, copy);
                     }
 
+					// Since we copy from a source group that is in selected
+					// state, but the copy is shown deselected in the viewer,
+					// We need to clear the selection flag here, else that
+					// prim never gets persisted at all. The client doesn't
+					// think it's selected, so it will never send a deselect...
+					copy.IsSelected=false;
+
                     m_numPrim++;
 
                     copy.StartScripts();

OpenSim/Region/Environment/Scenes/SceneObjectGroup.cs

@@ -1078,11 +1078,8 @@ namespace OpenSim.Region.Environment.Scenes
             // don't backup while it's selected or you're asking for changes mid stream.
             if (HasGroupChanged)
             {
-                // FIXME: Disabling this check temporarily since it seems that in some (as yet unidentified)
+                if ((!IsSelected) && (RootPart != null))
-                // circumstances with shift copy, we never register that some prims have been deselected, even though
+                {
-                // they are no longer selected in the client.
-//                if (!IsSelected)
-//                {
                     m_log.InfoFormat("[SCENE OBJECT GROUP]: Storing object {0}", UUID);
                     
                     SceneObjectGroup backup_group = Copy(OwnerID, GroupID, false);
@@ -1093,7 +1090,7 @@ namespace OpenSim.Region.Environment.Scenes
                     backup_group.ForEachPart(delegate(SceneObjectPart part) { part.ProcessInventoryBackup(datastore); });
                     
                     backup_group = null;
-//                }
+                }
 //                else
 //                {
 //                    m_log.DebugFormat(