diff --git a/.core_files.yaml b/.core_files.yaml
index 137bd44292b05..c6cd987616ad6 100644
--- a/.core_files.yaml
+++ b/.core_files.yaml
@@ -6,7 +6,7 @@ core: &core
   - homeassistant/helpers/*
   - homeassistant/package_constraints.txt
   - homeassistant/util/*
-  - pyproject.yaml
+  - pyproject.toml
   - requirements.txt
   - setup.cfg
 
diff --git a/homeassistant/components/harmony/subscriber.py b/homeassistant/components/harmony/subscriber.py
index b2652cc43d118..f71b486fd1687 100644
--- a/homeassistant/components/harmony/subscriber.py
+++ b/homeassistant/components/harmony/subscriber.py
@@ -2,6 +2,10 @@
 
 import asyncio
 import logging
+
+# pylint: disable-next=deprecated-typing-alias
+# Issue with Python 3.9.0 and 3.9.1 with collections.abc.Callable
+# https://bugs.python.org/issue42965
 from typing import Any, Callable, NamedTuple, Optional
 
 from homeassistant.core import callback
diff --git a/pyproject.toml b/pyproject.toml
index a2d7a8721b4b8..4f46f01854607 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -76,7 +76,6 @@ good-names = [
 # Enable once current issues are fixed:
 # consider-using-namedtuple-or-dataclass (Pylint CodeStyle extension)
 # consider-using-assignment-expr (Pylint CodeStyle extension)
-# deprecated-typing-alias (temporarily while updating code to Python 3.9)
 disable = [
     "format",
     "abstract-class-little-used",
@@ -102,7 +101,6 @@ disable = [
     "consider-using-f-string",
     "consider-using-namedtuple-or-dataclass",
     "consider-using-assignment-expr",
-    "deprecated-typing-alias",
 ]
 enable = [
     #"useless-suppression",  # temporarily every now and then to clean them up