diff --git a/gtk2_ardour/editor_ops.cc b/gtk2_ardour/editor_ops.cc
index 9bdd2e26a8..96ae169aed 100644
--- a/gtk2_ardour/editor_ops.cc
+++ b/gtk2_ardour/editor_ops.cc
@@ -3706,7 +3706,16 @@ Editor::remove_clicked_region ()
 
 	begin_reversible_command (_("remove region"));
 	playlist->clear_changes ();
+	playlist->clear_owned_changes ();
 	playlist->remove_region (clicked_regionview->region());
+
+	/* We might have removed regions, which alters other regions' layering_index,
+	   so we need to do a recursive diff here.
+	*/
+	vector<Command*> cmds;
+	playlist->rdiff (cmds);
+	_session->add_commands (cmds);
+	
 	_session->add_command(new StatefulDiffCommand (playlist));
 	commit_reversible_command ();
 }
@@ -3758,6 +3767,7 @@ Editor::remove_selected_regions ()
 		playlists.push_back (playlist);
 
 		playlist->clear_changes ();
+		playlist->clear_owned_changes ();
 		playlist->freeze ();
 		playlist->remove_region (*rl);
 	}
@@ -3766,6 +3776,14 @@ Editor::remove_selected_regions ()
 
 	for (pl = playlists.begin(); pl != playlists.end(); ++pl) {
 		(*pl)->thaw ();
+
+		/* We might have removed regions, which alters other regions' layering_index,
+		   so we need to do a recursive diff here.
+		*/
+		vector<Command*> cmds;
+		(*pl)->rdiff (cmds);
+		_session->add_commands (cmds);
+		
 		_session->add_command(new StatefulDiffCommand (*pl));
 	}
 
@@ -3812,6 +3830,7 @@ Editor::cut_copy_regions (CutCopyOp op, RegionSelection& rs)
 
 				if (fl == freezelist.end()) {
 					pl->clear_changes();
+					pl->clear_owned_changes ();
 					pl->freeze ();
 					freezelist.insert (pl);
 				}
@@ -3927,6 +3946,14 @@ Editor::cut_copy_regions (CutCopyOp op, RegionSelection& rs)
 
 	for (FreezeList::iterator pl = freezelist.begin(); pl != freezelist.end(); ++pl) {
 		(*pl)->thaw ();
+
+		/* We might have removed regions, which alters other regions' layering_index,
+		   so we need to do a recursive diff here.
+		*/
+		vector<Command*> cmds;
+		(*pl)->rdiff (cmds);
+		_session->add_commands (cmds);
+		
 		_session->add_command (new StatefulDiffCommand (*pl));
 	}
 }
@@ -4615,6 +4642,7 @@ Editor::apply_filter (Filter& filter, string command, ProgressReporter* progress
 			if (arv->audio_region()->apply (filter, progress) == 0) {
 
 				playlist->clear_changes ();
+				playlist->clear_owned_changes ();
 
 				if (filter.results.empty ()) {
 
@@ -4637,6 +4665,13 @@ Editor::apply_filter (Filter& filter, string command, ProgressReporter* progress
 
 				}
 
+				/* We might have removed regions, which alters other regions' layering_index,
+				   so we need to do a recursive diff here.
+				*/
+				vector<Command*> cmds;
+				playlist->rdiff (cmds);
+				_session->add_commands (cmds);
+				
 				_session->add_command(new StatefulDiffCommand (playlist));
 			} else {
 				goto out;
@@ -5716,6 +5751,7 @@ Editor::split_region_at_points (boost::shared_ptr<Region> r, AnalysisFeatureList
 	AnalysisFeatureList::const_iterator x;
 
 	pl->clear_changes ();
+	pl->clear_owned_changes ();
 
 	x = positions.begin();
 
@@ -5802,6 +5838,13 @@ Editor::split_region_at_points (boost::shared_ptr<Region> r, AnalysisFeatureList
 
 	pl->thaw ();
 
+	/* We might have removed regions, which alters other regions' layering_index,
+	   so we need to do a recursive diff here.
+	*/
+	vector<Command*> cmds;
+	pl->rdiff (cmds);
+	_session->add_commands (cmds);
+	
 	_session->add_command (new StatefulDiffCommand (pl));
 
 	if (select_new) {
diff --git a/libs/ardour/ardour/playlist.h b/libs/ardour/ardour/playlist.h
index 67cc1ccf54..626df720bd 100644
--- a/libs/ardour/ardour/playlist.h
+++ b/libs/ardour/ardour/playlist.h
@@ -378,6 +378,10 @@ public:
 	   with its constituent regions
 	*/
 	virtual void pre_uncombine (std::vector<boost::shared_ptr<Region> >&, boost::shared_ptr<Region>) {}
+
+private:
+
+	void setup_layering_indices (RegionList const &) const;
 };
 
 } /* namespace ARDOUR */
diff --git a/libs/ardour/playlist.cc b/libs/ardour/playlist.cc
index d3a461ea9e..c11e55779c 100644
--- a/libs/ardour/playlist.cc
+++ b/libs/ardour/playlist.cc
@@ -653,6 +653,7 @@ Playlist::flush_notifications (bool from_undo)
    PLAYLIST OPERATIONS
   *************************************************************/
 
+/** Note: this calls set_layer (..., DBL_MAX) so it will reset the layering index of region */
  void
  Playlist::add_region (boost::shared_ptr<Region> region, framepos_t position, float times, bool auto_partition)
  {
@@ -2097,7 +2098,7 @@ Playlist::flush_notifications (bool from_undo)
 	 freeze ();
 	 /* add the added regions */
 	 for (RegionListProperty::ChangeContainer::iterator i = change.added.begin(); i != change.added.end(); ++i) {
-		 add_region ((*i), (*i)->position());
+		 add_region_internal ((*i), (*i)->position());
 	 }
 	 /* remove the removed regions */
 	 for (RegionListProperty::ChangeContainer::iterator i = change.removed.begin(); i != change.removed.end(); ++i) {
@@ -2371,13 +2372,19 @@ Playlist::set_layer (boost::shared_ptr<Region> region, double new_layer)
 	
 	copy.insert (i, region);
 
-	/* Then re-write layering indices */
+	setup_layering_indices (copy);
+}
+
+void
+Playlist::setup_layering_indices (RegionList const & regions) const
+{
 	uint64_t j = 0;
-	for (RegionList::iterator k = copy.begin(); k != copy.end(); ++k) {
+	for (RegionList::const_iterator k = regions.begin(); k != regions.end(); ++k) {
 		(*k)->set_layering_index (j++);
 	}
 }
 
+
 /** Take the layering indices of each of our regions, compute the layers
  *  that they should be on, and write the layers back to the regions.
  */
@@ -2493,6 +2500,12 @@ Playlist::relayer ()
 	if (changed) {
 		notify_layering_changed ();
 	}
+
+	/* This relayer() may have been called as a result of a region removal, in which
+	   case we need to setup layering indices so account for the one that has just
+	   gone away.
+	*/
+	setup_layering_indices (copy);
 }
 
 void