diff --git a/.github/workflows/debug-artifacts-failure.yml b/.github/workflows/debug-artifacts-failure.yml
index bcc38d28aa..e6cddb0a87 100644
--- a/.github/workflows/debug-artifacts-failure.yml
+++ b/.github/workflows/debug-artifacts-failure.yml
@@ -50,7 +50,7 @@ jobs:
         run: ./build.sh
       - uses: ./../action/analyze
         id: analysis
-        env: 
+        env:
           # Forces a failure in this step.
           CODEQL_ACTION_EXTRA_OPTIONS: '{ "database": { "finalize": ["--invalid-option"] } }'
         with:
diff --git a/.github/workflows/debug-artifacts-legacy.yml b/.github/workflows/debug-artifacts-legacy.yml
index 2f024964b5..3ea3074bf6 100644
--- a/.github/workflows/debug-artifacts-legacy.yml
+++ b/.github/workflows/debug-artifacts-legacy.yml
@@ -56,7 +56,7 @@ jobs:
           debug-artifact-name: my-debug-artifacts
           debug-database-name: my-db
           # We manually exclude Swift from the languages list here, as it is not supported on Ubuntu
-          languages: cpp,csharp,go,java,javascript,python,ruby 
+          languages: cpp,csharp,go,java,javascript,python,ruby
       - name: Build code
         shell: bash
         run: ./build.sh
diff --git a/.github/workflows/debug-artifacts.yml b/.github/workflows/debug-artifacts.yml
index cd38ea506a..cfdf8e40d5 100644
--- a/.github/workflows/debug-artifacts.yml
+++ b/.github/workflows/debug-artifacts.yml
@@ -55,7 +55,7 @@ jobs:
           debug-artifact-name: my-debug-artifacts
           debug-database-name: my-db
           # We manually exclude Swift from the languages list here, as it is not supported on Ubuntu
-          languages: cpp,csharp,go,java,javascript,python,ruby 
+          languages: cpp,csharp,go,java,javascript,python,ruby
       - name: Build code
         shell: bash
         run: ./build.sh
diff --git a/pr-checks/sync.py b/pr-checks/sync.py
index c7b6abfdfc..37b120b439 100755
--- a/pr-checks/sync.py
+++ b/pr-checks/sync.py
@@ -4,6 +4,7 @@
 from ruamel.yaml.scalarstring import FoldedScalarString, SingleQuotedScalarString
 import pathlib
 import textwrap
+import os
 
 # The default set of CodeQL Bundle versions to use for the PR checks.
 defaultTestVersions = [
@@ -153,7 +154,8 @@ def writeHeader(checkStream):
         checkJob['env']['CODEQL_ACTION_TEST_MODE'] = True
     checkName = file.stem
 
-    with open(this_dir.parent / ".github" / "workflows" / f"__{checkName}.yml", 'w') as output_stream:
+    raw_file = this_dir.parent / ".github" / "workflows" / f"__{checkName}.yml.raw"
+    with open(raw_file, 'w') as output_stream:
         writeHeader(output_stream)
         yaml.dump({
             'name': f"PR Check - {checkSpecification['name']}",
@@ -175,3 +177,9 @@ def writeHeader(checkStream):
                 checkName: checkJob
             }
         }, output_stream)
+
+    with open(raw_file, 'r') as input_stream:
+        with open(this_dir.parent / ".github" / "workflows" / f"__{checkName}.yml", 'w') as output_stream:
+            content = input_stream.read()
+            output_stream.write("\n".join(list(map(lambda x:x.rstrip(), content.splitlines()))+['']))
+    os.remove(raw_file)