diff --git a/libs/ardour/monitor_port.cc b/libs/ardour/monitor_port.cc
index 45db2addb1..6dd6588155 100644
--- a/libs/ardour/monitor_port.cc
+++ b/libs/ardour/monitor_port.cc
@@ -338,6 +338,11 @@ MonitorPort::clear_ports (bool instantly)
 		MonitorInputChanged (i->first, false); /* EMIT SIGNAL */
 	}
 
+	if (instantly) {
+		/* release shared_ptr references */
+		_monitor_ports.flush ();
+	}
+
 	if (!s) {
 		return;
 	}
diff --git a/libs/ardour/port_manager.cc b/libs/ardour/port_manager.cc
index 7da3445f8f..db611aec91 100644
--- a/libs/ardour/port_manager.cc
+++ b/libs/ardour/port_manager.cc
@@ -1158,6 +1158,9 @@ PortManager::update_input_ports (bool clear)
 		 * do this when called from ::reestablish_ports()
 		 * "JACK: Cannot connect ports owned by inactive clients"
 		 */
+		/* .. but take the opportunity to clear out dead wood */
+		_audio_input_ports.flush ();
+		_midi_input_ports.flush ();
 		return;
 	}
 
diff --git a/libs/ardour/session_bundles.cc b/libs/ardour/session_bundles.cc
index e0bd838460..558c63716c 100644
--- a/libs/ardour/session_bundles.cc
+++ b/libs/ardour/session_bundles.cc
@@ -75,6 +75,7 @@ Session::remove_bundle (std::shared_ptr<Bundle> bundle)
 
 	if (removed) {
 		 BundleAddedOrRemoved (); /* EMIT SIGNAL */
+		 _bundles.flush ();
 	}
 
 	set_dirty();