diff --git a/.changeset/hmr-error-boundary.md b/.changeset/hmr-error-boundary.md
new file mode 100644
index 0000000000..b5d111361b
--- /dev/null
+++ b/.changeset/hmr-error-boundary.md
@@ -0,0 +1,5 @@
+---
+"@remix-run/router": patch
+---
+
+Fix HMR-driven error boundaries by properly reconstructing new routes and `manifest` in `\_internalSetRoutes`
diff --git a/packages/router/__tests__/router-test.ts b/packages/router/__tests__/router-test.ts
index 7720c49408..fd8d108c80 100644
--- a/packages/router/__tests__/router-test.ts
+++ b/packages/router/__tests__/router-test.ts
@@ -15351,7 +15351,7 @@ describe("a router", () => {
 
       // Routes should be updated
       expect(t.router.routes).not.toBe(ogRoutes);
-      expect(t.router.routes).toBe(newRoutes);
+      expect(t.router.routes).toEqual(newRoutes);
 
       // Loader data should be updated and foo removed
       expect(t.router.state.loaderData).toEqual({
@@ -15401,7 +15401,7 @@ describe("a router", () => {
 
       // Routes should be updated
       expect(t.router.routes).not.toBe(ogRoutes);
-      expect(t.router.routes).toBe(newRoutes);
+      expect(t.router.routes).toEqual(newRoutes);
 
       // Loader data should be updated
       expect(t.router.state.loaderData).toEqual({
@@ -15467,7 +15467,7 @@ describe("a router", () => {
 
       // Routes should be updated
       expect(t.router.routes).not.toBe(ogRoutes);
-      expect(t.router.routes).toBe(newRoutes);
+      expect(t.router.routes).toEqual(newRoutes);
 
       // Loader data should be updated
       expect(t.router.state.loaderData).toEqual({
@@ -15527,7 +15527,7 @@ describe("a router", () => {
 
       // Routes should be updated
       expect(t.router.routes).not.toBe(ogRoutes);
-      expect(t.router.routes).toBe(newRoutes);
+      expect(t.router.routes).toEqual(newRoutes);
 
       // Loader data should be updated
       expect(t.router.state.loaderData).toEqual({
@@ -15582,8 +15582,8 @@ describe("a router", () => {
         {
           path: "/",
           id: "root",
-          hasErrorBoundary: true,
           loader: () => rootDfd2.promise,
+          hasErrorBoundary: true,
           children: [
             {
               index: true,
@@ -15616,7 +15616,7 @@ describe("a router", () => {
 
       // Routes should be updated
       expect(currentRouter.routes).not.toEqual(ogRoutes);
-      expect(currentRouter.routes).toBe(newRoutes);
+      expect(currentRouter.routes).toEqual(newRoutes);
 
       // Loader data should be updated
       expect(currentRouter.state.loaderData).toEqual({
@@ -15684,12 +15684,13 @@ describe("a router", () => {
         {
           path: "/",
           id: "root",
-          hasErrorBoundary: true,
           loader: () => rootDfd2.promise,
+          hasErrorBoundary: true,
           children: [
             {
               index: true,
               id: "index",
+              hasErrorBoundary: false,
             },
           ],
         },
@@ -15711,7 +15712,7 @@ describe("a router", () => {
 
       // Routes should be updated
       expect(currentRouter.routes).not.toEqual(ogRoutes);
-      expect(currentRouter.routes).toBe(newRoutes);
+      expect(currentRouter.routes).toEqual(newRoutes);
 
       // Loader data should be updated
       expect(currentRouter.state.loaderData).toEqual({
diff --git a/packages/router/router.ts b/packages/router/router.ts
index 2fb88ccdde..545f006c63 100644
--- a/packages/router/router.ts
+++ b/packages/router/router.ts
@@ -2474,7 +2474,13 @@ export function createRouter(init: RouterInit): Router {
   }
 
   function _internalSetRoutes(newRoutes: AgnosticDataRouteObject[]) {
-    inFlightDataRoutes = newRoutes;
+    manifest = {};
+    inFlightDataRoutes = convertRoutesToDataRoutes(
+      newRoutes,
+      mapRouteProperties,
+      undefined,
+      manifest
+    );
   }
 
   router = {