diff --git a/lib/_update_javascripts.js b/lib/_update_javascripts.js
index d5242e0f26..9b27e89864 100644
--- a/lib/_update_javascripts.js
+++ b/lib/_update_javascripts.js
@@ -7,9 +7,12 @@ const path = require('path')
 const { projectDir, packageDir } = require('./path-utils')
 const updateDir = path.join(projectDir, 'update')
 
-async function fetchOriginal(filePath) {
-  const oldVersion = (await fs.readFile(path.join(projectDir, 'VERSION.txt'), 'utf8')).trim()
-  const remoteUrl = `https://raw.githubusercontent.com/alphagov/govuk-prototype-kit/v${oldVersion}/${filePath}`
+async function getProjectVersion () {
+  return (await fs.readFile(path.join(projectDir, 'VERSION.txt'), 'utf8')).trim()
+}
+
+async function fetchOriginal(version, filePath) {
+  const remoteUrl = `https://raw.githubusercontent.com/alphagov/govuk-prototype-kit/v${version}/${filePath}`
 
   let data = ''
   return new Promise((resolve, reject) => {
@@ -37,10 +40,20 @@ async function fetchOriginal(filePath) {
 }
 
 async function removeKitJsFromApplicationJs () {
+  const userVersion = getProjectVersion()
+
+  // If the user already has version 13 or greater of the kit installed then
+  // their application.js file is all their code and we don't don't want to
+  // change it
+  if (userVersion >= '13.0.0') {
+    return
+  }
+
   const assetPath = 'assets/javascripts/application.js'
-  const original = await fetchOriginal(path.posix.join('app', assetPath))
+  const original = await fetchOriginal(userVersion, path.posix.join('app', assetPath))
   const theirs = await fs.readFile(path.resolve(projectDir, 'app', assetPath), 'utf8')
 
+
   // If the user hasn't changed their application.js file we can just replace it completely
   if (original === theirs) {
     return fs.copyFile(path.join(packageDir, 'lib', assetPath), path.join(projectDir, 'app', assetPath))