diff --git a/lcviz/events.py b/lcviz/events.py
index 54f521ef..3ca014c6 100644
--- a/lcviz/events.py
+++ b/lcviz/events.py
@@ -1,18 +1,9 @@
 from glue.core.message import Message
 
-__all__ = ['ViewerRenamedMessage', 'EphemerisComponentChangedMessage',
+__all__ = ['EphemerisComponentChangedMessage',
            'EphemerisChangedMessage']
 
 
-class ViewerRenamedMessage(Message):
-    """Message emitted after a viewer is destroyed by the application."""
-    def __init__(self, old_viewer_ref, new_viewer_ref, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-
-        self.old_viewer_ref = old_viewer_ref
-        self.new_viewer_ref = new_viewer_ref
-
-
 class EphemerisComponentChangedMessage(Message):
     """Message emitted when an ephemeris component is added/renamed/removed in the
     ephemeris plugin"""
diff --git a/lcviz/helper.py b/lcviz/helper.py
index 6bc12845..565c3894 100644
--- a/lcviz/helper.py
+++ b/lcviz/helper.py
@@ -7,7 +7,6 @@
 from glue.core.component_id import ComponentID
 from glue.core.link_helpers import LinkSame
 from jdaviz.core.helpers import ConfigHelper
-from lcviz.events import ViewerRenamedMessage
 
 __all__ = ['LCviz']
 
@@ -47,46 +46,6 @@ def _get_range_subset_bounds(self, subset_state, *args, **kwargs):
              "subset_state": subset_state}]
 
 
-def _rename_viewer(app, old_reference, new_reference):
-    """
-    Rename a viewer.  If the ID and reference match, the ID will also be updated,
-    otherwise it will be kept.
-
-    CAUTION: use with caution as this does not currently update default
-    viewer reference names stored in helpers and could break behavior.
-
-    Parameters
-    ----------
-    old_reference : str
-        The current reference of the viewer
-    new_reference : str
-        The desired new reference name of the viewer
-    """
-    self = app
-    if new_reference in self.get_viewer_reference_names():
-        raise ValueError(f"viewer with reference='{new_reference}' already exists")
-    if new_reference in self.get_viewer_ids():
-        raise ValueError(f"viewer with id='{new_reference}' already exists")
-
-    viewer_item = self._get_viewer_item(old_reference)
-    old_id = viewer_item['id']
-
-    self._viewer_store[old_id]._reference_id = new_reference
-
-    viewer_item['reference'] = new_reference
-
-    if viewer_item['name'] == old_reference:
-        viewer_item['name'] = new_reference
-
-    if viewer_item['id'] == old_reference:
-        # update the id as well
-        viewer_item['id'] = new_reference
-        self._viewer_store[new_reference] = self._viewer_store.pop(old_id)
-        self.state.viewer_icons[new_reference] = self.state.viewer_icons.pop(old_id)
-
-    self.hub.broadcast(ViewerRenamedMessage(old_reference, new_reference, sender=self))
-
-
 def _link_new_data(app, reference_data=None, data_to_be_linked=None):
     dc = app.data_collection
     ref_data = dc[reference_data] if reference_data else dc[0]
@@ -135,11 +94,6 @@ def __init__(self, *args, **kwargs):
             lambda *args, **kwargs: _get_range_subset_bounds(self.app, *args, **kwargs)
         )
 
-        # TODO: remove this if/when jdaviz supports renaming viewers natively
-        self.app._rename_viewer = (
-            lambda *args, **kwargs: _rename_viewer(self.app, *args, **kwargs)
-        )
-
         self.app._link_new_data = (
             lambda *args, **kwargs: _link_new_data(self.app, *args, **kwargs)
         )
diff --git a/lcviz/plugins/binning/binning.py b/lcviz/plugins/binning/binning.py
index 5758d12b..49f796a0 100644
--- a/lcviz/plugins/binning/binning.py
+++ b/lcviz/plugins/binning/binning.py
@@ -144,13 +144,13 @@ def _live_update(self, event={}):
             times = lc_time
 
         for viewer_id, mark in self.marks.items():
+            viewer_ref = self.app.get_viewer_by_id(viewer_id).reference
             if self.ephemeris_selected == 'No ephemeris':
                 visible = True
-                # TODO: fix this to be general and not rely on ugly id
-                do_phase = viewer_id != 'lcviz-0'
+                do_phase = viewer_ref != 'flux-vs-time'
             else:
                 # TODO: try to fix flashing as traitlets update
-                visible = viewer_id.split(':')[-1] == self.ephemeris_selected
+                visible = viewer_ref.split(':')[-1] == self.ephemeris_selected
                 do_phase = False
 
             if visible:
diff --git a/lcviz/plugins/coords_info/coords_info.py b/lcviz/plugins/coords_info/coords_info.py
index 9ab33b4b..f7c8d44f 100644
--- a/lcviz/plugins/coords_info/coords_info.py
+++ b/lcviz/plugins/coords_info/coords_info.py
@@ -5,7 +5,6 @@
 from jdaviz.core.registries import tool_registry
 
 from lcviz.viewers import TimeScatterView, PhaseScatterView
-from lcviz.events import ViewerRenamedMessage
 
 
 __all__ = ['CoordsInfo']
@@ -19,10 +18,6 @@ class CoordsInfo(CoordsInfo):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
 
-        # TODO: move to jdaviz if/once viewer renaming supported
-        self.hub.subscribe(self, ViewerRenamedMessage,
-                           handler=self._viewer_renamed)
-
     def _viewer_renamed(self, msg):
         self._marks[msg.new_viewer_ref] = self._marks.pop(msg.old_viewer_ref)
 
diff --git a/lcviz/plugins/ephemeris/ephemeris.py b/lcviz/plugins/ephemeris/ephemeris.py
index d33b2f69..1ab10d49 100644
--- a/lcviz/plugins/ephemeris/ephemeris.py
+++ b/lcviz/plugins/ephemeris/ephemeris.py
@@ -317,8 +317,11 @@ def _on_component_add(self, lbl):
     def _on_component_rename(self, old_lbl, new_lbl):
         # this is triggered when the plugin component detects a change to the component name
         self._ephemerides[new_lbl] = self._ephemerides.pop(old_lbl, {})
-        if self._phase_viewer_id(old_lbl) in self.app.get_viewer_ids():
-            self.app._rename_viewer(self._phase_viewer_id(old_lbl), self._phase_viewer_id(new_lbl))
+        if self._phase_viewer_id(old_lbl) in self.app.get_viewer_reference_names():
+            self.app._update_viewer_reference_name(
+                self._phase_viewer_id(old_lbl),
+                self._phase_viewer_id(new_lbl)
+            )
 
         # update metadata entries so that they can be used for filtering applicable entries in
         # data menus
@@ -336,7 +339,7 @@ def _on_component_rename(self, old_lbl, new_lbl):
     def _on_component_remove(self, lbl):
         _ = self._ephemerides.pop(lbl, {})
         # remove the corresponding viewer, if it exists
-        viewer_item = self.app._viewer_item_by_id(self._phase_viewer_id(lbl))
+        viewer_item = self.app._viewer_item_by_reference(self._phase_viewer_id(lbl))
         if viewer_item is None:  # pragma: no cover
             return
         cid = viewer_item.get('id', None)
diff --git a/lcviz/template_mixin.py b/lcviz/template_mixin.py
index 6765d87f..97c56a7e 100644
--- a/lcviz/template_mixin.py
+++ b/lcviz/template_mixin.py
@@ -3,24 +3,12 @@
 from ipyvuetify import VuetifyTemplate
 from glue.core import HubListener
 
-import jdaviz
-from jdaviz.core.template_mixin import ViewerSelect, DatasetSelect, SelectPluginComponent
-from lcviz.events import ViewerRenamedMessage, EphemerisComponentChangedMessage
+from jdaviz.core.template_mixin import DatasetSelect, SelectPluginComponent
+from lcviz.events import EphemerisComponentChangedMessage
 
 __all__ = ['EphemerisSelect', 'EphemerisSelectMixin']
 
 
-# TODO: remove this if/when jdaviz supports renaming viewers natively
-class ViewerSelect(ViewerSelect):
-    def __init__(self, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.hub.subscribe(self, ViewerRenamedMessage, handler=self._on_viewers_changed)
-
-
-# monkey-patch upstream version so all plugins use the viewer-renamed logic
-jdaviz.core.template_mixin.ViewerSelect = ViewerSelect
-
-
 class EphemerisSelect(SelectPluginComponent):
     """
     Plugin select for ephemeris components defined by the Ephemeris plugin.