diff --git a/lms/djangoapps/commerce/api/v1/models.py b/lms/djangoapps/commerce/api/v1/models.py
index 21a24b4ab4..e956cfa370 100644
--- a/lms/djangoapps/commerce/api/v1/models.py
+++ b/lms/djangoapps/commerce/api/v1/models.py
@@ -107,8 +107,20 @@ class Course(object):
             merged_modes.add(merged_mode)
             merged_mode_keys.add(merged_mode.mode_slug)
 
-        deleted_modes = set(existing_modes.keys()) - merged_mode_keys
-        self._deleted_modes = [existing_modes[mode] for mode in deleted_modes]
+        # Masters degrees are not sold through the eCommerce site.
+        # So, Masters course modes are not included in PUT calls to this API,
+        # and their omission which would normally cause them to be deleted.
+        # We don't want that to happen, but for the time being,
+        # we cannot include in Masters modes in the PUT calls from eCommerce.
+        # So, here's hack to handle Masters course modes, along with any other
+        # modes that end up in that boat.
+        MODES_TO_NOT_DELETE = {
+            CourseMode.MASTERS,
+        }
+
+        modes_to_delete = set(existing_modes.keys()) - merged_mode_keys
+        modes_to_delete -= MODES_TO_NOT_DELETE
+        self._deleted_modes = [existing_modes[mode] for mode in modes_to_delete]
         self.modes = list(merged_modes)
 
     @classmethod
diff --git a/lms/djangoapps/commerce/api/v1/permissions.py b/lms/djangoapps/commerce/api/v1/permissions.py
index 1b5b41792d..019e111a02 100644
--- a/lms/djangoapps/commerce/api/v1/permissions.py
+++ b/lms/djangoapps/commerce/api/v1/permissions.py
@@ -24,6 +24,6 @@ class IsAuthenticatedOrActivationOverridden(BasePermission):
         if not request.user.is_authenticated and is_account_activation_requirement_disabled():
             try:
                 request.user = User.objects.get(id=request.session._session_cache['_auth_user_id'])
-            except DoesNotExist:
+            except User.DoesNotExist:
                 pass
         return request.user.is_authenticated
diff --git a/lms/djangoapps/commerce/api/v1/tests/test_views.py b/lms/djangoapps/commerce/api/v1/tests/test_views.py
index a23cc7506c..ad2e7c2cac 100644
--- a/lms/djangoapps/commerce/api/v1/tests/test_views.py
+++ b/lms/djangoapps/commerce/api/v1/tests/test_views.py
@@ -287,25 +287,45 @@ class CourseRetrieveUpdateViewTests(CourseApiViewTestMixin, ModuleStoreTestCase)
         self.assertIsNone(updated_verified_mode.expiration_datetime)
 
     def test_update_overwrite(self):
-        """ Verify that data submitted via PUT overwrites/deletes modes that are
-        not included in the body of the request. """
-        course_id = six.text_type(self.course.id)
-        expected_course_mode = CourseMode(
+        """
+        Verify that data submitted via PUT overwrites/deletes modes that are
+        not included in the body of the request, EXCEPT the Masters mode,
+        which it leaves alone.
+        """
+        existing_mode = self.course_mode
+        existing_masters_mode = CourseMode.objects.create(
+            course_id=self.course.id,
+            mode_slug=u'masters',
+            min_price=10000,
+            currency=u'USD',
+            sku=u'DEF456',
+            bulk_sku=u'BULK-DEF456'
+        )
+        new_mode = CourseMode(
+            course_id=self.course.id,
             mode_slug=u'credit',
             min_price=500,
             currency=u'USD',
             sku=u'ABC123',
             bulk_sku=u'BULK-ABC123'
         )
-        expected = self._serialize_course(self.course, [expected_course_mode])
-        path = reverse('commerce_api:v1:courses:retrieve_update', args=[course_id])
-        response = self.client.put(path, json.dumps(expected), content_type=JSON_CONTENT_TYPE)
-        self.assertEqual(response.status_code, 200)
-        actual = json.loads(response.content)
-        self.assertEqual(actual, expected)
 
-        # The existing CourseMode should have been removed.
-        self.assertFalse(CourseMode.objects.filter(id=self.course_mode.id).exists())
+        path = reverse('commerce_api:v1:courses:retrieve_update', args=[six.text_type(self.course.id)])
+        data = json.dumps(self._serialize_course(self.course, [new_mode]))
+        response = self.client.put(path, data, content_type=JSON_CONTENT_TYPE)
+        self.assertEqual(response.status_code, 200)
+
+        # Check modes list in response, disregarding its order.
+        expected_dict = self._serialize_course(self.course, [new_mode])
+        expected_items = expected_dict['modes']
+        actual_items = json.loads(response.content)['modes']
+        self.assertCountEqual(actual_items, expected_items)
+
+        # The existing non-Masters CourseMode should have been removed.
+        self.assertFalse(CourseMode.objects.filter(id=existing_mode.id).exists())
+
+        # The existing Masters course mode should remain.
+        self.assertTrue(CourseMode.objects.filter(id=existing_masters_mode.id).exists())
 
     @ddt.data(*itertools.product(
         ('honor', 'audit', 'verified', 'professional', 'no-id-professional'),