diff --git a/keyboards/0xcb/1337/config.h b/keyboards/0xcb/1337/config.h
index 21332c5585..d134d1ab49 100644
--- a/keyboards/0xcb/1337/config.h
+++ b/keyboards/0xcb/1337/config.h
@@ -37,10 +37,9 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
     { E6, B4, B2 } \
 }
 #define TAP_CODE_DELAY 10
-#define ENCODER_DIRECTION_FLIP
 #define ENCODER_RESOLUTION 4
-#define ENCODERS_PAD_A { F5 }
-#define ENCODERS_PAD_B { F6 }
+#define ENCODERS_PAD_A { F6 }
+#define ENCODERS_PAD_B { F5 }
 
 #define BACKLIGHT_PIN B5
 #define BACKLIGHT_BREATHING
diff --git a/keyboards/absinthe/config.h b/keyboards/absinthe/config.h
index 3000a4b8a1..d6acd350cc 100644
--- a/keyboards/absinthe/config.h
+++ b/keyboards/absinthe/config.h
@@ -44,10 +44,8 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #define MATRIX_COL_PINS { F4, F5, F6, F7, B1, B3, B2, D3, D0 }
 #define UNUSED_PINS
 
-#define ENCODERS_PAD_A { D5 }
-#define ENCODERS_PAD_B { B7 }
-
-#define ENCODER_DIRECTION_FLIP
+#define ENCODERS_PAD_A { B7 }
+#define ENCODERS_PAD_B { D5 }
 
 /* COL2ROW, ROW2COL*/
 #define DIODE_DIRECTION COL2ROW
diff --git a/keyboards/aplyard/aplx6/rev2/config.h b/keyboards/aplyard/aplx6/rev2/config.h
index b4bb7d62ad..2b30e67e09 100644
--- a/keyboards/aplyard/aplx6/rev2/config.h
+++ b/keyboards/aplyard/aplx6/rev2/config.h
@@ -41,9 +41,8 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #define TAPPING_TERM 200
 
 /* Encoder */
-#define ENCODERS_PAD_A { F4 }
-#define ENCODERS_PAD_B { F5 }
+#define ENCODERS_PAD_A { F5 }
+#define ENCODERS_PAD_B { F4 }
 #define ENCODER_RESOLUTION 4
-#define ENCODER_DIRECTION_FLIP
 
 #define TAP_CODE_DELAY 50
diff --git a/keyboards/basketweave/config.h b/keyboards/basketweave/config.h
index afe66c6b14..cdaffe4ca3 100644
--- a/keyboards/basketweave/config.h
+++ b/keyboards/basketweave/config.h
@@ -50,10 +50,9 @@
  */
 // #define GRAVE_ESC_CTRL_OVERRIDE
 
-#define ENCODERS_PAD_A { D7 }
-#define ENCODERS_PAD_B { C0 }
+#define ENCODERS_PAD_A { C0 }
+#define ENCODERS_PAD_B { D7 }
 #define ENCODER_RESOLUTION 4
-#define ENCODER_DIRECTION_FLIP
 #define TAP_CODE_DELAY 10
 
 /* Bootmagic Lite key configuration */
diff --git a/keyboards/keysofkings/twokey/config.h b/keyboards/keysofkings/twokey/config.h
index 9b77fa73e2..29612187f8 100755
--- a/keyboards/keysofkings/twokey/config.h
+++ b/keyboards/keysofkings/twokey/config.h
@@ -35,10 +35,9 @@
 #define UNUSED_PINS
 
 
-#define ENCODERS_PAD_A { E6 }
-#define ENCODERS_PAD_B { D7 }
+#define ENCODERS_PAD_A { D7 }
+#define ENCODERS_PAD_B { E6 }
 #define ENCODER_RESOLUTION 1
-#define ENCODER_DIRECTION_FLIP
 
 /* COL2ROW or ROW2COL */
 #define DIODE_DIRECTION COL2ROW
diff --git a/keyboards/makrosu/config.h b/keyboards/makrosu/config.h
index 8a5214fe68..b587477f8a 100644
--- a/keyboards/makrosu/config.h
+++ b/keyboards/makrosu/config.h
@@ -34,9 +34,8 @@
 #define MATRIX_COL_PINS { B2, B3, B1, F7, F6, F5}
 #define UNUSED_PINS
 
-#define ENCODERS_PAD_A { D1 }
-#define ENCODERS_PAD_B { E6 }
-#define ENCODER_DIRECTION_FLIP
+#define ENCODERS_PAD_A { E6 }
+#define ENCODERS_PAD_B { D1 }
 #define TAP_CODE_DELAY 10 
 /* COL2ROW or ROW2COL */
 #define DIODE_DIRECTION COL2ROW
diff --git a/keyboards/ramonimbao/herringbone/pro/config.h b/keyboards/ramonimbao/herringbone/pro/config.h
index 25249456f9..20f92282b0 100644
--- a/keyboards/ramonimbao/herringbone/pro/config.h
+++ b/keyboards/ramonimbao/herringbone/pro/config.h
@@ -48,10 +48,8 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #define DIODE_DIRECTION COL2ROW
 
 /* Encoder pin assignment */
-#define ENCODERS_PAD_A { C3 }
-#define ENCODERS_PAD_B { C2 }
-
-#define ENCODER_DIRECTION_FLIP
+#define ENCODERS_PAD_A { C2 }
+#define ENCODERS_PAD_B { C3 }
 
 /* Debounce reduces chatter (unintended double-presses) - set 0 if debouncing is not needed */
 #define DEBOUNCE 5
diff --git a/keyboards/space_space/rev2/config.h b/keyboards/space_space/rev2/config.h
index 66f8f6add4..bb8f04da2b 100644
--- a/keyboards/space_space/rev2/config.h
+++ b/keyboards/space_space/rev2/config.h
@@ -41,12 +41,11 @@
 
 /* ROTARY ENCODERS */
 #define ENCODERS_PAD_A \
-    { D7, F7 }
-#define ENCODERS_PAD_B \
     { B4, C7 }
+#define ENCODERS_PAD_B \
+    { D7, F7 }
 
 #define ENCODER_RESOLUTION 3
-#define ENCODER_DIRECTION_FLIP
 
 #define DEBOUNCE 5
 
diff --git a/keyboards/synapse/config.h b/keyboards/synapse/config.h
index 82a0aadea5..809194afe8 100644
--- a/keyboards/synapse/config.h
+++ b/keyboards/synapse/config.h
@@ -41,12 +41,11 @@
 
 /* ROTARY ENCODERS */
 #define ENCODERS_PAD_A \
-    { D6, C6 }
-#define ENCODERS_PAD_B \
     { D7, C7 }
+#define ENCODERS_PAD_B \
+    { D6, C6 }
 
 #define ENCODER_RESOLUTION 4
-#define ENCODER_DIRECTION_FLIP
 
 #define DEBOUNCE 5
 
diff --git a/keyboards/z12/config.h b/keyboards/z12/config.h
index 7f897b795d..68aff7acf7 100644
--- a/keyboards/z12/config.h
+++ b/keyboards/z12/config.h
@@ -25,9 +25,8 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #define MANUFACTURER    zigotica
 #define PRODUCT         z12
 
-#define ENCODERS_PAD_A { B4, B2 }
-#define ENCODERS_PAD_B { B5, B6 }
-#define ENCODER_DIRECTION_FLIP
+#define ENCODERS_PAD_A { B5, B6 }
+#define ENCODERS_PAD_B { B4, B2 }
 
 /* key matrix size */
 #define MATRIX_ROWS 4
diff --git a/lib/python/qmk/cli/format/c.py b/lib/python/qmk/cli/format/c.py
index 0160e6036f..568684ed56 100644
--- a/lib/python/qmk/cli/format/c.py
+++ b/lib/python/qmk/cli/format/c.py
@@ -74,7 +74,7 @@ def filter_files(files, core_only=False):
             # The following statement checks each file to see if the file path is
             # - in the core directories
             # - not in the ignored directories
-            if not any(i in str(file) for i in core_dirs) or any(i in str(file) for i in ignored):
+            if not any(str(file).startswith(i) for i in core_dirs) or any(str(file).startswith(i) for i in ignored):
                 files[index] = None
                 cli.log.debug("Skipping non-core file %s, as '--core-only' is used.", file)