BUG: stack changes NA values in the index

doc/source/whatsnew/v2.2.0.rst

@@ -686,6 +686,7 @@ Reshaping
 - Bug in :meth:`DataFrame.melt` where it would not preserve the datetime (:issue:`55254`)
 - Bug in :meth:`DataFrame.pivot_table` where the row margin is incorrect when the columns have numeric names (:issue:`26568`)
 - Bug in :meth:`DataFrame.pivot` with numeric columns and extension dtype for data (:issue:`56528`)
+- Bug in :meth:`DataFrame.stack` and :meth:`Series.stack` with ``future_stack=True`` would not preserve NA values in the index (:issue:`56573`)
 
 Sparse
 ^^^^^^

pandas/core/reshape/reshape.py

@@ -953,8 +953,8 @@ def stack_v3(frame: DataFrame, level: list[int]) -> Series | DataFrame:
         index_levels = frame.index.levels
         index_codes = list(np.tile(frame.index.codes, (1, ratio)))
     else:
-        index_levels = [frame.index.unique()]
-        codes = factorize(frame.index)[0]
+        codes, uniques = factorize(frame.index, use_na_sentinel=False)
+        index_levels = [uniques]
         index_codes = list(np.tile(codes, (1, ratio)))
     if isinstance(stack_cols, MultiIndex):
         column_levels = ordered_stack_cols.levels

pandas/tests/frame/test_stack_unstack.py

@@ -2638,3 +2638,41 @@ def test_stack_tuple_columns(future_stack):
         ),
     )
     tm.assert_series_equal(result, expected)
+
+
+@pytest.mark.parametrize(
+    "dtype, na_value",
+    [
+        ("float64", np.nan),
+        ("Float64", np.nan),
+        ("Float64", pd.NA),
+        ("Int64", pd.NA),
+    ],
+)
+@pytest.mark.parametrize("test_multiindex", [True, False])
+def test_stack_preserves_na(dtype, na_value, test_multiindex):
+    # GH#56573
+    if test_multiindex:
+        index = MultiIndex.from_arrays(2 * [Index([na_value], dtype=dtype)])
+    else:
+        index = Index([na_value], dtype=dtype)
+    df = DataFrame({"a": [1]}, index=index)
+    result = df.stack(future_stack=True)
+
+    if test_multiindex:
+        expected_index = MultiIndex.from_arrays(
+            [
+                Index([na_value], dtype=dtype),
+                Index([na_value], dtype=dtype),
+                Index(["a"]),
+            ]
+        )
+    else:
+        expected_index = MultiIndex.from_arrays(
+            [
+                Index([na_value], dtype=dtype),
+                Index(["a"]),
+            ]
+        )
+    expected = Series(1, index=expected_index)
+    tm.assert_series_equal(result, expected)