diff --git a/src/automated-pipelines/lib/update-markdown.js b/src/automated-pipelines/lib/update-markdown.js
index b10c6cf449..72d42348b0 100644
--- a/src/automated-pipelines/lib/update-markdown.js
+++ b/src/automated-pipelines/lib/update-markdown.js
@@ -11,8 +11,7 @@ import { allVersions } from '../../../lib/all-versions.js'
 import getApplicableVersions from '../../../lib/get-applicable-versions.js'
 
 const ROOT_INDEX_FILE = 'content/index.md'
-export const MARKDOWN_COMMENT =
-  '\n\n<!-- Content after this section is automatically generated -->\n\n'
+export const MARKDOWN_COMMENT = '\n<!-- Content after this section is automatically generated -->\n'
 
 // Main entrypoint into this module. This function adds, removes, and updates
 // versions frontmatter in all directories under the targetDirectory.
@@ -100,11 +99,15 @@ async function updateMarkdownFile(
       throw new Error(`Error: ${file} has multiple comment delimiters`)
     }
 
-    // Only proceed if the content or versions have changed
-    const [manuallyCreatedContent, automatedContent] = content.split(commentDelimiter)
+    const [manuallyCreatedContent, automatedContent] = matches
+      ? content.split(commentDelimiter)
+      : [content, '']
+
+    const isDelimiterMissing = !matches
     const isContentSame = automatedContent === sourceContent
     const isVersionsSame = isEqual(sourceData.versions, data.versions)
-    if (isContentSame && isVersionsSame) {
+    // Only proceed if the content or versions have changed
+    if (isContentSame && isVersionsSame && !isDelimiterMissing) {
       return
     }
 
@@ -116,7 +119,7 @@ async function updateMarkdownFile(
     await writeFile(file, matter.stringify(targetContent, newData))
   } else {
     await createDirectory(path.dirname(file))
-    await writeFile(file, matter.stringify(sourceContent, sourceData))
+    await writeFile(file, matter.stringify(commentDelimiter + sourceContent, sourceData))
   }
 }
 
diff --git a/src/codeql-cli/scripts/sync.js b/src/codeql-cli/scripts/sync.js
index 6528ec1dfd..8900fb1e38 100755
--- a/src/codeql-cli/scripts/sync.js
+++ b/src/codeql-cli/scripts/sync.js
@@ -17,7 +17,7 @@ const { targetDirectory, sourceDirectory, frontmatterDefaults, markdownPrefix }
 )
 const SOURCE_REPO = sourceDirectory.split('/')[0]
 const TEMP_DIRECTORY = path.join(SOURCE_REPO, 'tempCliDocs')
-const MARKDOWN_PREFIX = `${markdownPrefix}\n\n`
+const MARKDOWN_PREFIX = `\n${markdownPrefix}\n\n`
 
 main()
 
diff --git a/src/rest/scripts/utils/update-markdown.js b/src/rest/scripts/utils/update-markdown.js
index 923d48e1b8..b790e236ce 100644
--- a/src/rest/scripts/utils/update-markdown.js
+++ b/src/rest/scripts/utils/update-markdown.js
@@ -5,7 +5,6 @@ import { readFile } from 'fs/promises'
 import {
   updateContentDirectory,
   convertVersionsToFrontmatter,
-  MARKDOWN_COMMENT,
 } from '../../../automated-pipelines/lib/update-markdown.js'
 import { getDocsVersion } from '../../../../lib/all-versions.js'
 import { REST_DATA_DIR, REST_SCHEMA_FILENAME } from '../../lib/index.js'
@@ -102,7 +101,7 @@ async function getMarkdownContent(versions) {
           ),
           ...frontmatterDefaults,
         },
-        content: MARKDOWN_COMMENT,
+        content: '',
       }
       continue
     }
@@ -118,7 +117,7 @@ async function getMarkdownContent(versions) {
           versions: await convertVersionsToFrontmatter(versions[category][subcategory].versions),
           ...frontmatterDefaults,
         },
-        content: MARKDOWN_COMMENT,
+        content: '',
       }
     }
   }