diff --git a/apps/ui/src/components/views/project-settings-view/project-bulk-replace-dialog.tsx b/apps/ui/src/components/views/project-settings-view/project-bulk-replace-dialog.tsx
index 12881adf..66e2cb0e 100644
--- a/apps/ui/src/components/views/project-settings-view/project-bulk-replace-dialog.tsx
+++ b/apps/ui/src/components/views/project-settings-view/project-bulk-replace-dialog.tsx
@@ -121,11 +121,12 @@ export function ProjectBulkReplaceDialog({
   // Find the model from provider that maps to a specific Claude model
   const findModelForClaudeAlias = (
     provider: ClaudeCompatibleProvider | null,
-    claudeAlias: ClaudeModelAlias
+    claudeAlias: ClaudeModelAlias,
+    phase: PhaseModelKey
   ): PhaseModelEntry => {
     if (!provider) {
-      // Anthropic Direct - use Claude model directly
-      return { model: claudeAlias };
+      // Anthropic Direct - reset to default phase model (includes correct thinking levels)
+      return DEFAULT_PHASE_MODELS[phase];
     }
 
     // Find model that maps to this Claude alias
@@ -152,7 +153,7 @@ export function ProjectBulkReplaceDialog({
       const globalEntry = phaseModels[phase] ?? DEFAULT_PHASE_MODELS[phase];
       const currentEntry = projectOverrides[phase] || globalEntry;
       const claudeAlias = getClaudeModelAlias(currentEntry);
-      const newEntry = findModelForClaudeAlias(selectedProviderConfig, claudeAlias);
+      const newEntry = findModelForClaudeAlias(selectedProviderConfig, claudeAlias, phase);
 
       // Get display names
       const getCurrentDisplay = (): string => {
@@ -175,7 +176,9 @@ export function ProjectBulkReplaceDialog({
       };
 
       const isChanged =
-        currentEntry.model !== newEntry.model || currentEntry.providerId !== newEntry.providerId;
+        currentEntry.model !== newEntry.model ||
+        currentEntry.providerId !== newEntry.providerId ||
+        currentEntry.thinkingLevel !== newEntry.thinkingLevel;
 
       return {
         phase,
diff --git a/apps/ui/src/components/views/settings-view/model-defaults/bulk-replace-dialog.tsx b/apps/ui/src/components/views/settings-view/model-defaults/bulk-replace-dialog.tsx
index 10ac8836..aafd383d 100644
--- a/apps/ui/src/components/views/settings-view/model-defaults/bulk-replace-dialog.tsx
+++ b/apps/ui/src/components/views/settings-view/model-defaults/bulk-replace-dialog.tsx
@@ -112,11 +112,12 @@ export function BulkReplaceDialog({ open, onOpenChange }: BulkReplaceDialogProps
   // Find the model from provider that maps to a specific Claude model
   const findModelForClaudeAlias = (
     provider: ClaudeCompatibleProvider | null,
-    claudeAlias: ClaudeModelAlias
+    claudeAlias: ClaudeModelAlias,
+    phase: PhaseModelKey
   ): PhaseModelEntry => {
     if (!provider) {
-      // Anthropic Direct - use Claude model directly
-      return { model: claudeAlias };
+      // Anthropic Direct - reset to default phase model (includes correct thinking levels)
+      return DEFAULT_PHASE_MODELS[phase];
     }
 
     // Find model that maps to this Claude alias
@@ -141,7 +142,7 @@ export function BulkReplaceDialog({ open, onOpenChange }: BulkReplaceDialogProps
     return ALL_PHASES.map((phase) => {
       const currentEntry = phaseModels[phase] ?? DEFAULT_PHASE_MODELS[phase];
       const claudeAlias = getClaudeModelAlias(currentEntry);
-      const newEntry = findModelForClaudeAlias(selectedProviderConfig, claudeAlias);
+      const newEntry = findModelForClaudeAlias(selectedProviderConfig, claudeAlias, phase);
 
       // Get display names
       const getCurrentDisplay = (): string => {
@@ -164,7 +165,9 @@ export function BulkReplaceDialog({ open, onOpenChange }: BulkReplaceDialogProps
       };
 
       const isChanged =
-        currentEntry.model !== newEntry.model || currentEntry.providerId !== newEntry.providerId;
+        currentEntry.model !== newEntry.model ||
+        currentEntry.providerId !== newEntry.providerId ||
+        currentEntry.thinkingLevel !== newEntry.thinkingLevel;
 
       return {
         phase,
diff --git a/libs/utils/src/atomic-writer.ts b/libs/utils/src/atomic-writer.ts
index fe07e5eb..9fc7ff4a 100644
--- a/libs/utils/src/atomic-writer.ts
+++ b/libs/utils/src/atomic-writer.ts
@@ -7,6 +7,7 @@
 
 import { secureFs } from '@automaker/platform';
 import path from 'path';
+import crypto from 'crypto';
 import { createLogger } from './logger.js';
 import { mkdirSafe } from './fs-utils.js';
 
@@ -99,7 +100,9 @@ export async function atomicWriteJson<T>(
 ): Promise<void> {
   const { indent = 2, createDirs = false, backupCount = 0 } = options;
   const resolvedPath = path.resolve(filePath);
-  const tempPath = `${resolvedPath}.tmp.${Date.now()}`;
+  // Use timestamp + random suffix to ensure uniqueness even for concurrent writes
+  const uniqueSuffix = `${Date.now()}.${crypto.randomBytes(4).toString('hex')}`;
+  const tempPath = `${resolvedPath}.tmp.${uniqueSuffix}`;
 
   // Create parent directories if requested
   if (createDirs) {
diff --git a/package-lock.json b/package-lock.json
index 64192c40..c86ba4aa 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -6218,6 +6218,7 @@
       "version": "19.2.7",
       "resolved": "https://registry.npmjs.org/@types/react/-/react-19.2.7.tgz",
       "integrity": "sha512-MWtvHrGZLFttgeEj28VXHxpmwYbor/ATPYbBfSFZEIRK0ecCFLl2Qo55z52Hss+UV9CRN7trSeq1zbgx7YDWWg==",
+      "dev": true,
       "license": "MIT",
       "dependencies": {
         "csstype": "^3.2.2"
@@ -6227,7 +6228,7 @@
       "version": "19.2.3",
       "resolved": "https://registry.npmjs.org/@types/react-dom/-/react-dom-19.2.3.tgz",
       "integrity": "sha512-jp2L/eY6fn+KgVVQAOqYItbF0VY/YApe5Mz2F0aykSO8gx31bYCZyvSeYxCHKvzHG5eZjc+zyaS5BrBWya2+kQ==",
-      "devOptional": true,
+      "dev": true,
       "license": "MIT",
       "peerDependencies": {
         "@types/react": "^19.2.0"
@@ -8438,6 +8439,7 @@
       "version": "3.2.3",
       "resolved": "https://registry.npmjs.org/csstype/-/csstype-3.2.3.tgz",
       "integrity": "sha512-z1HGKcYy2xA8AGQfwrn0PAy+PB7X/GSj3UVJW9qKyn43xWa+gl5nXmU4qqLMRzWVLFC8KusUX8T/0kCiOYpAIQ==",
+      "dev": true,
       "license": "MIT"
     },
     "node_modules/d3-color": {
@@ -11331,7 +11333,6 @@
       "os": [
         "android"
       ],
-      "peer": true,
       "engines": {
         "node": ">= 12.0.0"
       },
@@ -11353,7 +11354,6 @@
       "os": [
         "darwin"
       ],
-      "peer": true,
       "engines": {
         "node": ">= 12.0.0"
       },
@@ -11375,7 +11375,6 @@
       "os": [
         "darwin"
       ],
-      "peer": true,
       "engines": {
         "node": ">= 12.0.0"
       },
@@ -11397,7 +11396,6 @@
       "os": [
         "freebsd"
       ],
-      "peer": true,
       "engines": {
         "node": ">= 12.0.0"
       },
@@ -11419,7 +11417,6 @@
       "os": [
         "linux"
       ],
-      "peer": true,
       "engines": {
         "node": ">= 12.0.0"
       },
@@ -11441,7 +11438,6 @@
       "os": [
         "linux"
       ],
-      "peer": true,
       "engines": {
         "node": ">= 12.0.0"
       },
@@ -11463,7 +11459,6 @@
       "os": [
         "linux"
       ],
-      "peer": true,
       "engines": {
         "node": ">= 12.0.0"
       },
@@ -11485,7 +11480,6 @@
       "os": [
         "linux"
       ],
-      "peer": true,
       "engines": {
         "node": ">= 12.0.0"
       },
@@ -11507,7 +11501,6 @@
       "os": [
         "linux"
       ],
-      "peer": true,
       "engines": {
         "node": ">= 12.0.0"
       },
@@ -11529,7 +11522,6 @@
       "os": [
         "win32"
       ],
-      "peer": true,
       "engines": {
         "node": ">= 12.0.0"
       },
@@ -11551,7 +11543,6 @@
       "os": [
         "win32"
       ],
-      "peer": true,
       "engines": {
         "node": ">= 12.0.0"
       },