diff --git a/Makefile b/Makefile
index db1066b2ef..f3e4d80b36 100644
--- a/Makefile
+++ b/Makefile
@@ -67,7 +67,7 @@ marlin:
 .PHONY: marlin
 
 clean:
-	rm -r .pio/build
+	rm -rf .pio/build*
 
 tests-single-ci:
 	export GIT_RESET_HARD=true
diff --git a/buildroot/bin/ci_src_filter b/buildroot/bin/ci_src_filter
index 1043e57d81..566e3e1e95 100755
--- a/buildroot/bin/ci_src_filter
+++ b/buildroot/bin/ci_src_filter
@@ -6,7 +6,9 @@ set -e
 FN="platformio.ini"
 
 if [[ $1 == "-n" ]]; then
-  awk '/default_src_filter/ { sub("default_src_filter", "org_src_filter"); print "default_src_filter = +<src/*>"; } 1' $FN > $FN~ && mv $FN~ $FN
+  if ! grep -q "org_src_filter" "$FN"; then
+    awk '/default_src_filter/ { sub("default_src_filter", "org_src_filter"); print "default_src_filter = +<src/*>"; } 1' $FN > $FN~ && mv $FN~ $FN
+  fi
 else
   git checkout $FN 2>/dev/null
 fi
diff --git a/buildroot/bin/restore_configs b/buildroot/bin/restore_configs
index 0bbd36fd1c..041ef045da 100755
--- a/buildroot/bin/restore_configs
+++ b/buildroot/bin/restore_configs
@@ -3,31 +3,34 @@
 import os, sys, subprocess
 
 files_to_remove = [
-  "Marlin/_Bootscreen.h",
-  "Marlin/_Statusscreen.h",
-  "marlin_config.json",
-  ".pio/build/mc.zip"
+    "Marlin/_Bootscreen.h",
+    "Marlin/_Statusscreen.h",
+    "marlin_config.json",
+    ".pio/build/mc.zip"
 ]
 
 for file in files_to_remove:
-  if os.path.exists(file):
-    os.remove(file)
+    if os.path.exists(file):
+        os.remove(file)
 
 def use_example_configs():
-  try:
-    subprocess.run(['use_example_configs'], check=True)
-  except FileNotFoundError:
-    print("use_example_configs not found, skipping.")
-  pass
+    try:
+        subprocess.run(['use_example_configs'], check=True)
+    except FileNotFoundError:
+        try:
+            subprocess.run(['./buildroot/bin/use_example_configs'], check=True)
+        except FileNotFoundError:
+            print("use_example_configs not found, skipping.")
+    pass
 
 if len(sys.argv) > 1 and sys.argv[1] in ['-d', '--default']:
-  use_example_configs()
+    use_example_configs()
 else:
-  files_to_checkout = [
-    "Marlin/Configuration.h",
-    "Marlin/Configuration_adv.h",
-    "Marlin/config.ini",
-    "Marlin/src/pins/*/pins_*.h"
-  ]
-  for file in files_to_checkout:
-    subprocess.run(["git", "checkout", file], stderr=subprocess.DEVNULL)
+    files_to_checkout = [
+        "Marlin/Configuration.h",
+        "Marlin/Configuration_adv.h",
+        "Marlin/config.ini",
+        "Marlin/src/pins/*/pins_*.h"
+    ]
+    for file in files_to_checkout:
+        subprocess.run(["git", "checkout", file], stderr=subprocess.DEVNULL)