diff --git a/packages/router-core/src/route.ts b/packages/router-core/src/route.ts
index b67651cbb0f..4b4e4404cc3 100644
--- a/packages/router-core/src/route.ts
+++ b/packages/router-core/src/route.ts
@@ -1709,15 +1709,6 @@ export class BaseRoute<
     this._to = fullPath as TrimPathRight<TFullPath>
   }
 
-  clone = (other: typeof this) => {
-    this._path = other._path
-    this._id = other._id
-    this._fullPath = other._fullPath
-    this._to = other._to
-    this.options.getParentRoute = other.options.getParentRoute
-    this.children = other.children
-  }
-
   addChildren: RouteAddChildrenFn<
     TRegister,
     TParentRoute,
diff --git a/packages/router-plugin/src/core/code-splitter/compilers.ts b/packages/router-plugin/src/core/code-splitter/compilers.ts
index 5c2da5d3907..b5ade26a12d 100644
--- a/packages/router-plugin/src/core/code-splitter/compilers.ts
+++ b/packages/router-plugin/src/core/code-splitter/compilers.ts
@@ -133,6 +133,7 @@ export function compileCodeSplitReferenceRoute(
   let createRouteFn: string
 
   let modified = false as boolean
+  let hmrAdded = false as boolean
   babel.traverse(ast, {
     Program: {
       enter(programPath) {
@@ -182,9 +183,10 @@ export function compileCodeSplitReferenceRoute(
                 }
                 if (!splittableCreateRouteFns.includes(createRouteFn)) {
                   // we can't split this route but we still add HMR handling if enabled
-                  if (opts.addHmr) {
-                    modified = true
+                  if (opts.addHmr && !hmrAdded) {
                     programPath.pushContainer('body', routeHmrStatement)
+                    modified = true
+                    hmrAdded = true
                   }
                   // exit traversal so this route is not split
                   return programPath.stop()
@@ -307,8 +309,10 @@ export function compileCodeSplitReferenceRoute(
                         )()
 
                         // add HMR handling
-                        if (opts.addHmr) {
+                        if (opts.addHmr && !hmrAdded) {
                           programPath.pushContainer('body', routeHmrStatement)
+                          modified = true
+                          hmrAdded = true
                         }
                       } else {
                         // if (splitNodeMeta.splitStrategy === 'lazyFn') {
diff --git a/packages/router-plugin/src/core/route-hmr-statement.ts b/packages/router-plugin/src/core/route-hmr-statement.ts
index 2815b892729..3080c17a19a 100644
--- a/packages/router-plugin/src/core/route-hmr-statement.ts
+++ b/packages/router-plugin/src/core/route-hmr-statement.ts
@@ -1,13 +1,44 @@
 import * as template from '@babel/template'
+import type { AnyRoute } from '@tanstack/router-core'
+
+type AnyRouteWithPrivateProps = AnyRoute & {
+  _path: string
+  _id: string
+  _fullPath: string
+  _to: string
+}
+
+function handleRouteUpdate(
+  oldRoute: AnyRouteWithPrivateProps,
+  newRoute: AnyRouteWithPrivateProps,
+) {
+  newRoute._path = oldRoute._path
+  newRoute._id = oldRoute._id
+  newRoute._fullPath = oldRoute._fullPath
+  newRoute._to = oldRoute._to
+  newRoute.children = oldRoute.children
+  newRoute.parentRoute = oldRoute.parentRoute
+
+  const router = window.__TSR_ROUTER__!
+  router.routesById[newRoute.id] = newRoute
+  router.routesByPath[newRoute.fullPath] = newRoute
+  const oldRouteIndex = router.flatRoutes.indexOf(oldRoute)
+  if (oldRouteIndex > -1) {
+    router.flatRoutes[oldRouteIndex] = newRoute
+  }
+  router.invalidate({ filter: (m) => m.routeId === oldRoute.id })
+}
 
 export const routeHmrStatement = template.statement(
   `
 if (import.meta.hot) {
   import.meta.hot.accept((newModule) => {
-    if (newModule && newModule.Route && typeof newModule.Route.clone === 'function') {
-      newModule.Route.clone(Route)
+    if (Route && newModule && newModule.Route) {
+      (${handleRouteUpdate.toString()})(Route, newModule.Route)
     }
    })
 }
 `,
+  // Disable placeholder parsing so identifiers like __TSR_ROUTER__ are treated as normal identifiers instead of template placeholders
+  { placeholderPattern: false },
 )()
diff --git a/packages/router-plugin/tests/add-hmr/snapshots/react/arrow-function@true.tsx b/packages/router-plugin/tests/add-hmr/snapshots/react/arrow-function@true.tsx
index c73adc15365..3ba73b49a83 100644
--- a/packages/router-plugin/tests/add-hmr/snapshots/react/arrow-function@true.tsx
+++ b/packages/router-plugin/tests/add-hmr/snapshots/react/arrow-function@true.tsx
@@ -9,8 +9,26 @@ export const Route = createFileRoute('/posts')({
 });
 if (import.meta.hot) {
   import.meta.hot.accept(newModule => {
-    if (newModule && newModule.Route && typeof newModule.Route.clone === 'function') {
-      newModule.Route.clone(Route);
+    if (Route && newModule && newModule.Route) {
+      (function handleRouteUpdate(oldRoute, newRoute) {
+        newRoute._path = oldRoute._path;
+        newRoute._id = oldRoute._id;
+        newRoute._fullPath = oldRoute._fullPath;
+        newRoute._to = oldRoute._to;
+        newRoute.children = oldRoute.children;
+        newRoute.parentRoute = oldRoute.parentRoute;
+        const router = window.__TSR_ROUTER__;
+        router.routesById[newRoute.id] = newRoute;
+        router.routesByPath[newRoute.fullPath] = newRoute;
+        const oldRouteIndex = router.flatRoutes.indexOf(oldRoute);
+        if (oldRouteIndex > -1) {
+          router.flatRoutes[oldRouteIndex] = newRoute;
+        }
+        ;
+        router.invalidate({
+          filter: m => m.routeId === oldRoute.id
+        });
+      })(Route, newModule.Route);
     }
   });
 }
\ No newline at end of file
diff --git a/packages/router-plugin/tests/add-hmr/snapshots/react/function-declaration@true.tsx b/packages/router-plugin/tests/add-hmr/snapshots/react/function-declaration@true.tsx
index 9d1550f3671..534faf3c154 100644
--- a/packages/router-plugin/tests/add-hmr/snapshots/react/function-declaration@true.tsx
+++ b/packages/router-plugin/tests/add-hmr/snapshots/react/function-declaration@true.tsx
@@ -9,8 +9,26 @@ export const Route = createFileRoute('/posts')({
 });
 if (import.meta.hot) {
   import.meta.hot.accept(newModule => {
-    if (newModule && newModule.Route && typeof newModule.Route.clone === 'function') {
-      newModule.Route.clone(Route);
+    if (Route && newModule && newModule.Route) {
+      (function handleRouteUpdate(oldRoute, newRoute) {
+        newRoute._path = oldRoute._path;
+        newRoute._id = oldRoute._id;
+        newRoute._fullPath = oldRoute._fullPath;
+        newRoute._to = oldRoute._to;
+        newRoute.children = oldRoute.children;
+        newRoute.parentRoute = oldRoute.parentRoute;
+        const router = window.__TSR_ROUTER__;
+        router.routesById[newRoute.id] = newRoute;
+        router.routesByPath[newRoute.fullPath] = newRoute;
+        const oldRouteIndex = router.flatRoutes.indexOf(oldRoute);
+        if (oldRouteIndex > -1) {
+          router.flatRoutes[oldRouteIndex] = newRoute;
+        }
+        ;
+        router.invalidate({
+          filter: m => m.routeId === oldRoute.id
+        });
+      })(Route, newModule.Route);
     }
   });
 }
\ No newline at end of file
diff --git a/packages/router-plugin/tests/add-hmr/snapshots/solid/arrow-function@true.tsx b/packages/router-plugin/tests/add-hmr/snapshots/solid/arrow-function@true.tsx
index faada7e55bb..3b42bca7c45 100644
--- a/packages/router-plugin/tests/add-hmr/snapshots/solid/arrow-function@true.tsx
+++ b/packages/router-plugin/tests/add-hmr/snapshots/solid/arrow-function@true.tsx
@@ -8,8 +8,26 @@ export const Route = createFileRoute('/posts')({
 });
 if (import.meta.hot) {
   import.meta.hot.accept(newModule => {
-    if (newModule && newModule.Route && typeof newModule.Route.clone === 'function') {
-      newModule.Route.clone(Route);
+    if (Route && newModule && newModule.Route) {
+      (function handleRouteUpdate(oldRoute, newRoute) {
+        newRoute._path = oldRoute._path;
+        newRoute._id = oldRoute._id;
+        newRoute._fullPath = oldRoute._fullPath;
+        newRoute._to = oldRoute._to;
+        newRoute.children = oldRoute.children;
+        newRoute.parentRoute = oldRoute.parentRoute;
+        const router = window.__TSR_ROUTER__;
+        router.routesById[newRoute.id] = newRoute;
+        router.routesByPath[newRoute.fullPath] = newRoute;
+        const oldRouteIndex = router.flatRoutes.indexOf(oldRoute);
+        if (oldRouteIndex > -1) {
+          router.flatRoutes[oldRouteIndex] = newRoute;
+        }
+        ;
+        router.invalidate({
+          filter: m => m.routeId === oldRoute.id
+        });
+      })(Route, newModule.Route);
     }
   });
 }
\ No newline at end of file