diff --git a/src/cliproxy/executor/index.ts b/src/cliproxy/executor/index.ts
index c61add33..2d76146c 100644
--- a/src/cliproxy/executor/index.ts
+++ b/src/cliproxy/executor/index.ts
@@ -363,6 +363,7 @@ export async function execClaudeWithCLIProxy(
     thinkingParse.value,
     process.env.CCS_THINKING
   );
+  const thinkingCfg = getThinkingConfig();
 
   if (thinkingParse.duplicateDisplays.length > 0) {
     console.warn(
@@ -813,7 +814,6 @@ export async function execClaudeWithCLIProxy(
           process.env.CCS_CODEX_REASONING_TRACE === '1' ||
           process.env.CCS_CODEX_REASONING_TRACE === 'true';
         const stripPathPrefix = useRemoteProxy ? '/api/provider/codex' : undefined;
-        const thinkingCfg = getThinkingConfig();
         const codexThinkingOff = shouldDisableCodexReasoning(thinkingCfg, thinkingOverride);
         codexReasoningProxy = new CodexReasoningProxy({
           upstreamBaseUrl: postSanitizationBaseUrl,
@@ -889,9 +889,8 @@ export async function execClaudeWithCLIProxy(
 
   // 11b. Print thinking status feedback (TTY only, non-piped sessions)
   if (process.stderr.isTTY) {
-    const thinkingCfgStatus = getThinkingConfig();
     const { thinkingLabel, sourceLabel } = buildThinkingStartupStatus(
-      thinkingCfgStatus,
+      thinkingCfg,
       thinkingOverride,
       thinkingSource,
       thinkingParse.sourceDisplay
diff --git a/src/cliproxy/executor/thinking-override-resolver.ts b/src/cliproxy/executor/thinking-override-resolver.ts
index e0957710..593187e1 100644
--- a/src/cliproxy/executor/thinking-override-resolver.ts
+++ b/src/cliproxy/executor/thinking-override-resolver.ts
@@ -18,7 +18,7 @@ export function parseEnvThinkingOverride(raw: string | undefined): string | numb
   const trimmed = raw.trim();
   if (!trimmed) return undefined;
 
-  if (/^-?\d+$/.test(trimmed)) {
+  if (/^\d+$/.test(trimmed)) {
     const parsed = Number.parseInt(trimmed, 10);
     if (parsed < THINKING_BUDGET_MIN || parsed > THINKING_BUDGET_MAX) {
       return undefined;
diff --git a/src/commands/config-thinking-command.ts b/src/commands/config-thinking-command.ts
index c1b27b4d..36b55b41 100644
--- a/src/commands/config-thinking-command.ts
+++ b/src/commands/config-thinking-command.ts
@@ -13,7 +13,11 @@ import {
 } from '../config/unified-config-loader';
 import { DEFAULT_THINKING_TIER_DEFAULTS } from '../config/unified-config-types';
 import { VALID_THINKING_LEVELS } from '../cliproxy/thinking-validator';
-import { parseThinkingCommandArgs, parseThinkingOverrideInput } from './config-thinking-parser';
+import {
+  clearProviderOverride,
+  parseThinkingCommandArgs,
+  parseThinkingOverrideInput,
+} from './config-thinking-parser';
 
 const VALID_THINKING_MODES = ['auto', 'off', 'manual'] as const;
 
@@ -271,27 +275,21 @@ export async function handleConfigThinkingCommand(args: string[]): Promise<void>
       process.exitCode = 1;
       return;
     }
-    const currentOverrides = thinkingConfig.provider_overrides ?? {};
-    const nextOverrides = { ...currentOverrides };
-    if (!nextOverrides[provider]) {
-      // no-op, but still considered change request to keep command deterministic
-      hasChanges = true;
-    } else if (!tier) {
-      delete nextOverrides[provider];
+    const normalizedTier = tier as ThinkingTier | undefined;
+    const clearResult = clearProviderOverride(
+      thinkingConfig.provider_overrides,
+      provider,
+      normalizedTier
+    );
+    thinkingConfig.provider_overrides = clearResult.nextOverrides;
+    if (clearResult.changed) {
       hasChanges = true;
     } else {
-      const normalizedTier = tier as ThinkingTier;
-      const providerEntry = { ...nextOverrides[provider] };
-      delete providerEntry[normalizedTier];
-      if (Object.keys(providerEntry).length === 0) {
-        delete nextOverrides[provider];
-      } else {
-        nextOverrides[provider] = providerEntry;
-      }
-      hasChanges = true;
+      console.log(
+        info(`No provider override found for '${provider}'${tier ? ` tier '${tier}'` : ''}`)
+      );
+      console.log('');
     }
-    thinkingConfig.provider_overrides =
-      Object.keys(nextOverrides).length > 0 ? nextOverrides : undefined;
   }
 
   if (hasChanges) {
diff --git a/src/commands/config-thinking-parser.ts b/src/commands/config-thinking-parser.ts
index 2d82c253..15ffd83a 100644
--- a/src/commands/config-thinking-parser.ts
+++ b/src/commands/config-thinking-parser.ts
@@ -15,6 +15,10 @@ interface ThinkingCommandOptions {
   help?: boolean;
 }
 
+type ThinkingTier = 'opus' | 'sonnet' | 'haiku';
+export type ThinkingTierOverrideMap = Partial<Record<ThinkingTier, string>>;
+export type ThinkingProviderOverrides = Record<string, ThinkingTierOverrideMap>;
+
 export interface ParseResult {
   options: ThinkingCommandOptions;
   error?: string;
@@ -107,3 +111,48 @@ export function parseThinkingOverrideInput(rawOverride: string): {
     error: `Invalid override: ${rawOverride}`,
   };
 }
+
+export function clearProviderOverride(
+  currentOverrides: ThinkingProviderOverrides | undefined,
+  provider: string,
+  tier?: ThinkingTier
+): { nextOverrides: ThinkingProviderOverrides | undefined; changed: boolean } {
+  const current = currentOverrides ?? {};
+  const nextOverrides: ThinkingProviderOverrides = { ...current };
+
+  const providerEntry = nextOverrides[provider];
+  if (!providerEntry) {
+    return {
+      nextOverrides: Object.keys(nextOverrides).length > 0 ? nextOverrides : undefined,
+      changed: false,
+    };
+  }
+
+  if (!tier) {
+    delete nextOverrides[provider];
+    return {
+      nextOverrides: Object.keys(nextOverrides).length > 0 ? nextOverrides : undefined,
+      changed: true,
+    };
+  }
+
+  if (providerEntry[tier] === undefined) {
+    return {
+      nextOverrides: Object.keys(nextOverrides).length > 0 ? nextOverrides : undefined,
+      changed: false,
+    };
+  }
+
+  const nextProviderEntry = { ...providerEntry };
+  delete nextProviderEntry[tier];
+  if (Object.keys(nextProviderEntry).length === 0) {
+    delete nextOverrides[provider];
+  } else {
+    nextOverrides[provider] = nextProviderEntry;
+  }
+
+  return {
+    nextOverrides: Object.keys(nextOverrides).length > 0 ? nextOverrides : undefined,
+    changed: true,
+  };
+}
diff --git a/src/web-server/routes/misc-routes.ts b/src/web-server/routes/misc-routes.ts
index 8d680051..fb3037c9 100644
--- a/src/web-server/routes/misc-routes.ts
+++ b/src/web-server/routes/misc-routes.ts
@@ -26,6 +26,20 @@ import { validateFilePath } from './route-helpers';
 
 const router = Router();
 
+export function resolveThinkingProviderOverridesForSave(
+  currentProviderOverrides: ThinkingConfig['provider_overrides'] | undefined,
+  updatesProviderOverrides: Record<string, Partial<ThinkingConfig['tier_defaults']>> | undefined,
+  shouldClearProviderOverrides: boolean
+): ThinkingConfig['provider_overrides'] | undefined {
+  if (shouldClearProviderOverrides) {
+    return undefined;
+  }
+  if (updatesProviderOverrides !== undefined) {
+    return updatesProviderOverrides;
+  }
+  return currentProviderOverrides;
+}
+
 // ==================== Generic File API ====================
 
 /**
@@ -437,11 +451,11 @@ router.put('/thinking', (req: Request, res: Response): void => {
         sonnet: updates.tier_defaults?.sonnet ?? config.thinking?.tier_defaults?.sonnet ?? 'medium',
         haiku: updates.tier_defaults?.haiku ?? config.thinking?.tier_defaults?.haiku ?? 'low',
       },
-      provider_overrides: shouldClearProviderOverrides
-        ? undefined
-        : updates.provider_overrides !== undefined
-          ? normalizedProviderOverrides
-          : config.thinking?.provider_overrides,
+      provider_overrides: resolveThinkingProviderOverridesForSave(
+        config.thinking?.provider_overrides,
+        updates.provider_overrides !== undefined ? normalizedProviderOverrides : undefined,
+        shouldClearProviderOverrides
+      ),
       show_warnings: updates.show_warnings ?? config.thinking?.show_warnings ?? true,
     };
 
diff --git a/tests/unit/cliproxy/codex-reasoning-proxy-extended-context.test.ts b/tests/unit/cliproxy/codex-reasoning-proxy-extended-context.test.ts
index 09eb8c53..1e6f0cd3 100644
--- a/tests/unit/cliproxy/codex-reasoning-proxy-extended-context.test.ts
+++ b/tests/unit/cliproxy/codex-reasoning-proxy-extended-context.test.ts
@@ -5,6 +5,11 @@ import {
   CodexReasoningProxy,
   getEffortForModel,
 } from '../../../src/cliproxy/codex-reasoning-proxy';
+import {
+  parseEnvThinkingOverride,
+  resolveRuntimeThinkingOverride,
+  shouldDisableCodexReasoning,
+} from '../../../src/cliproxy/executor/thinking-override-resolver';
 
 type JsonRecord = Record<string, unknown>;
 
@@ -224,4 +229,122 @@ describe('CodexReasoningProxy extended-context compatibility', () => {
     expect(response.statusCode).toBe(200);
     expect(capturedBody?.model).toBe('enterprise-internal-high');
   });
+
+  it('keeps reasoning enabled when CCS_THINKING=high overrides config off', async () => {
+    let capturedBody: JsonRecord | null = null;
+
+    expect(parseEnvThinkingOverride('high')).toBe('high');
+    const { thinkingOverride } = resolveRuntimeThinkingOverride(undefined, 'high');
+    const disableEffort = shouldDisableCodexReasoning(
+      {
+        mode: 'off',
+        tier_defaults: {
+          opus: 'high',
+          sonnet: 'medium',
+          haiku: 'low',
+        },
+        show_warnings: true,
+      },
+      thinkingOverride
+    );
+
+    const upstream = http.createServer((req, res) => {
+      let rawBody = '';
+      req.setEncoding('utf8');
+      req.on('data', (chunk) => {
+        rawBody += chunk;
+      });
+      req.on('end', () => {
+        capturedBody = rawBody ? (JSON.parse(rawBody) as JsonRecord) : {};
+        res.writeHead(200, { 'Content-Type': 'application/json' });
+        res.end(JSON.stringify({ ok: true }));
+      });
+    });
+    cleanupServers.push(upstream);
+
+    const upstreamPort = await listenOnRandomPort(upstream);
+    const proxy = new CodexReasoningProxy({
+      upstreamBaseUrl: `http://127.0.0.1:${upstreamPort}`,
+      disableEffort,
+      defaultEffort: 'medium',
+      modelMap: {
+        defaultModel: 'gpt-5.3-codex',
+      },
+    });
+
+    const proxyPort = await proxy.start();
+    const response = await postJson(
+      `http://127.0.0.1:${proxyPort}/api/provider/codex/v1/messages`,
+      {
+        model: 'gpt-5.3-codex-high',
+        messages: [],
+      }
+    );
+
+    proxy.stop();
+
+    expect(response.statusCode).toBe(200);
+    expect(disableEffort).toBe(false);
+    expect(capturedBody?.model).toBe('gpt-5.3-codex');
+    expect((capturedBody?.reasoning as JsonRecord | undefined)?.effort).toBe('high');
+  });
+
+  it('disables reasoning when CCS_THINKING=off is provided', async () => {
+    let capturedBody: JsonRecord | null = null;
+
+    expect(parseEnvThinkingOverride('off')).toBe('off');
+    const { thinkingOverride } = resolveRuntimeThinkingOverride(undefined, 'off');
+    const disableEffort = shouldDisableCodexReasoning(
+      {
+        mode: 'auto',
+        tier_defaults: {
+          opus: 'high',
+          sonnet: 'medium',
+          haiku: 'low',
+        },
+        show_warnings: true,
+      },
+      thinkingOverride
+    );
+
+    const upstream = http.createServer((req, res) => {
+      let rawBody = '';
+      req.setEncoding('utf8');
+      req.on('data', (chunk) => {
+        rawBody += chunk;
+      });
+      req.on('end', () => {
+        capturedBody = rawBody ? (JSON.parse(rawBody) as JsonRecord) : {};
+        res.writeHead(200, { 'Content-Type': 'application/json' });
+        res.end(JSON.stringify({ ok: true }));
+      });
+    });
+    cleanupServers.push(upstream);
+
+    const upstreamPort = await listenOnRandomPort(upstream);
+    const proxy = new CodexReasoningProxy({
+      upstreamBaseUrl: `http://127.0.0.1:${upstreamPort}`,
+      disableEffort,
+      defaultEffort: 'medium',
+      modelMap: {
+        defaultModel: 'gpt-5.3-codex',
+      },
+    });
+
+    const proxyPort = await proxy.start();
+    const response = await postJson(
+      `http://127.0.0.1:${proxyPort}/api/provider/codex/v1/messages`,
+      {
+        model: 'gpt-5.3-codex-high',
+        messages: [],
+      }
+    );
+
+    proxy.stop();
+
+    expect(response.statusCode).toBe(200);
+    expect(disableEffort).toBe(true);
+    expect(capturedBody?.model).toBe('gpt-5.3-codex');
+    expect((capturedBody?.reasoning as JsonRecord | undefined)?.effort).toBeUndefined();
+  });
 });
diff --git a/tests/unit/commands/config-thinking-command.test.ts b/tests/unit/commands/config-thinking-command.test.ts
index a549c99b..e98efedb 100644
--- a/tests/unit/commands/config-thinking-command.test.ts
+++ b/tests/unit/commands/config-thinking-command.test.ts
@@ -3,6 +3,7 @@ import {
   parseThinkingCommandArgs,
   parseThinkingOverrideInput,
 } from '../../../src/commands/config-thinking-command';
+import { clearProviderOverride } from '../../../src/commands/config-thinking-parser';
 
 describe('config thinking command parser', () => {
   it('rejects missing required option values', () => {
@@ -41,3 +42,47 @@ describe('config thinking override normalization', () => {
     expect(parseThinkingOverrideInput('8192')).toEqual({ value: 8192 });
   });
 });
+
+describe('config thinking provider override clearing', () => {
+  it('is a no-op when provider override does not exist', () => {
+    const result = clearProviderOverride(
+      {
+        codex: { opus: 'high' },
+      },
+      'gemini'
+    );
+
+    expect(result.changed).toBe(false);
+    expect(result.nextOverrides).toEqual({
+      codex: { opus: 'high' },
+    });
+  });
+
+  it('is a no-op when provider exists but tier override does not', () => {
+    const result = clearProviderOverride(
+      {
+        codex: { opus: 'high' },
+      },
+      'codex',
+      'haiku'
+    );
+
+    expect(result.changed).toBe(false);
+    expect(result.nextOverrides).toEqual({
+      codex: { opus: 'high' },
+    });
+  });
+
+  it('removes provider entry when last tier is cleared', () => {
+    const result = clearProviderOverride(
+      {
+        codex: { opus: 'high' },
+      },
+      'codex',
+      'opus'
+    );
+
+    expect(result.changed).toBe(true);
+    expect(result.nextOverrides).toBeUndefined();
+  });
+});
diff --git a/tests/unit/web-server/thinking-routes-logic.test.ts b/tests/unit/web-server/thinking-routes-logic.test.ts
new file mode 100644
index 00000000..e98b734c
--- /dev/null
+++ b/tests/unit/web-server/thinking-routes-logic.test.ts
@@ -0,0 +1,42 @@
+import { describe, expect, it } from 'bun:test';
+import { resolveThinkingProviderOverridesForSave } from '../../../src/web-server/routes/misc-routes';
+
+describe('thinking routes logic', () => {
+  it('clears provider overrides when clear flag is set', () => {
+    const result = resolveThinkingProviderOverridesForSave(
+      {
+        codex: { opus: 'high' },
+      },
+      {
+        gemini: { sonnet: 'medium' },
+      },
+      true
+    );
+
+    expect(result).toBeUndefined();
+  });
+
+  it('applies normalized updates when provided and clear flag is false', () => {
+    const updates = {
+      gemini: { sonnet: 'medium' },
+    };
+    const result = resolveThinkingProviderOverridesForSave(
+      {
+        codex: { opus: 'high' },
+      },
+      updates,
+      false
+    );
+
+    expect(result).toEqual(updates);
+  });
+
+  it('preserves current overrides when no updates are provided', () => {
+    const current = {
+      codex: { opus: 'high' },
+    };
+    const result = resolveThinkingProviderOverridesForSave(current, undefined, false);
+
+    expect(result).toEqual(current);
+  });
+});