diff --git a/packages/ui/src/components/sections/agents/AgentsPage.tsx b/packages/ui/src/components/sections/agents/AgentsPage.tsx
index 5d7b182a..277fe1e6 100644
--- a/packages/ui/src/components/sections/agents/AgentsPage.tsx
+++ b/packages/ui/src/components/sections/agents/AgentsPage.tsx
@@ -578,6 +578,7 @@ export const AgentsPage: React.FC = () => {
 
     try {
       const trimmedModel = model.trim();
+      const trimmedPrompt = prompt.trim();
       const permissionConfig = buildPermissionConfigWithGlobal(globalPermission, permissionRules);
       const config: AgentConfig = {
         name: agentName,
@@ -586,7 +587,7 @@ export const AgentsPage: React.FC = () => {
         model: trimmedModel === '' ? null : trimmedModel,
         temperature,
         top_p: topP,
-        prompt: prompt.trim() || undefined,
+        prompt: trimmedPrompt || (isNewAgent ? undefined : null),
         permission: permissionConfig,
         scope: isNewAgent ? draftScope : undefined,
       };
diff --git a/packages/ui/src/components/update/OpenCodeUpdateToast.tsx b/packages/ui/src/components/update/OpenCodeUpdateToast.tsx
index f6deda11..7a4a321c 100644
--- a/packages/ui/src/components/update/OpenCodeUpdateToast.tsx
+++ b/packages/ui/src/components/update/OpenCodeUpdateToast.tsx
@@ -38,7 +38,7 @@ export const OpenCodeUpdateToast: React.FC = () => {
       message: t('opencodeUpdate.toast.reload.message'),
       mode: 'projects',
       scopes: ['all'],
-    });
+    }).catch(() => undefined);
   }, [t]);
 
   const runUpgrade = React.useCallback(async () => {
diff --git a/packages/ui/src/components/views/SettingsView.tsx b/packages/ui/src/components/views/SettingsView.tsx
index b11bafa7..a07d43ff 100644
--- a/packages/ui/src/components/views/SettingsView.tsx
+++ b/packages/ui/src/components/views/SettingsView.tsx
@@ -749,7 +749,7 @@ export const SettingsView: React.FC<SettingsViewProps> = ({ onClose, forceMobile
                       'text-sm font-semibold text-sidebar-foreground/90',
                       'hover:text-sidebar-foreground hover:bg-interactive-hover',
                     )}
-                    onClick={() => void reloadOpenCodeConfiguration({ message: 'Restarting OpenCode…', mode: 'projects', scopes: ['all'] })}
+                    onClick={() => void reloadOpenCodeConfiguration({ message: 'Restarting OpenCode…', mode: 'projects', scopes: ['all'] }).catch(() => undefined)}
                   >
                     <Icon name="restart" className="h-4 w-4 shrink-0" />
                     <span>{t('settings.view.actions.reloadOpenCode')}</span>
diff --git a/packages/ui/src/stores/useAgentsStore.ts b/packages/ui/src/stores/useAgentsStore.ts
index 0f4fe455..aa083528 100644
--- a/packages/ui/src/stores/useAgentsStore.ts
+++ b/packages/ui/src/stores/useAgentsStore.ts
@@ -11,10 +11,10 @@ import {
 } from "@/lib/configUpdate";
 import { getSafeStorage } from "./utils/safeStorage";
 import { useConfigStore } from "@/stores/useConfigStore";
-import { useCommandsStore } from "@/stores/useCommandsStore";
+import { invalidateCommandsLoadCache, useCommandsStore } from "@/stores/useCommandsStore";
 import { useProjectsStore } from "@/stores/useProjectsStore";
 import { useSkillsCatalogStore } from "@/stores/useSkillsCatalogStore";
-import { useSkillsStore } from "@/stores/useSkillsStore";
+import { invalidateSkillsLoadCache, useSkillsStore } from "@/stores/useSkillsStore";
 import { runtimeFetch } from "@/lib/runtime-fetch";
 
 // Note: useDirectoryStore cannot be imported at top level to avoid circular dependency
@@ -106,7 +106,7 @@ export interface AgentConfig {
   model?: string | null;
   temperature?: number;
   top_p?: number;
-  prompt?: string;
+  prompt?: string | null;
   mode?: "primary" | "subagent" | "all";
   permission?: PermissionConfig | null;
 
@@ -364,7 +364,7 @@ export const useAgentsStore = create<AgentsStore>()(
                 message: payload?.message,
                 delayMs: payload?.reloadDelayMs,
                 scopes: ["agents"],
-                mode: "active",
+                mode: "projects",
               });
               return true;
             }
@@ -426,7 +426,7 @@ export const useAgentsStore = create<AgentsStore>()(
                 message: payload?.message,
                 delayMs: payload?.reloadDelayMs,
                 scopes: ["agents"],
-                mode: "active",
+                mode: "projects",
               });
               return true;
             }
@@ -473,7 +473,7 @@ export const useAgentsStore = create<AgentsStore>()(
                 message: payload?.message,
                 delayMs: payload?.reloadDelayMs,
                 scopes: ["agents"],
-                mode: "active",
+                mode: "projects",
               });
               return true;
             }
@@ -648,18 +648,21 @@ async function performConfigRefresh(options: {
       uiRefreshTasks.push(agentConfigStore.loadAgents().then(() => undefined));
     }
     if (refreshCommands) {
+      invalidateCommandsLoadCache(currentDirectory);
       uiRefreshTasks.push(commandsStore.loadCommands().then(() => undefined));
     }
     if (refreshSkills) {
+      invalidateSkillsLoadCache(currentDirectory);
       uiRefreshTasks.push(skillsStore.loadSkills().then(() => undefined));
-      uiRefreshTasks.push(skillsCatalogStore.loadCatalog().then(() => undefined));
+      uiRefreshTasks.push(skillsCatalogStore.loadCatalog({ refresh: true }).then(() => undefined));
     }
 
     updateConfigUpdateMessage("Refreshing configuration…");
     await Promise.all([...sdkRefreshTasks, ...uiRefreshTasks]);
-  } catch {
+  } catch (error) {
     updateConfigUpdateMessage("OpenCode refresh failed. Please retry.");
     await sleep(1500);
+    throw error;
   } finally {
     finishConfigUpdate();
   }
diff --git a/packages/ui/src/stores/useCommandsStore.ts b/packages/ui/src/stores/useCommandsStore.ts
index 92306b55..a3accc94 100644
--- a/packages/ui/src/stores/useCommandsStore.ts
+++ b/packages/ui/src/stores/useCommandsStore.ts
@@ -47,6 +47,10 @@ const getCommandsCacheKey = (directory: string | null): string => {
   return directory?.trim() || DEFAULT_COMMANDS_CACHE_KEY;
 };
 
+export const invalidateCommandsLoadCache = (directory: string | null = getRequestDirectory()) => {
+  commandsLastLoadedAt.delete(getCommandsCacheKey(directory));
+};
+
 const buildCommandsSignature = (commands: Command[]): string => {
   return commands
     .map((command) => [
@@ -277,6 +281,7 @@ export const useCommandsStore = create<CommandsStore>()(
             console.log('[CommandsStore] Command created successfully');
 
             const needsReload = payload?.requiresReload ?? true;
+            invalidateCommandsLoadCache(directory);
             if (needsReload) {
               requiresReload = true;
               await performFullConfigRefresh({
@@ -338,6 +343,7 @@ export const useCommandsStore = create<CommandsStore>()(
             console.log('[CommandsStore] Command updated successfully');
 
             const needsReload = payload?.requiresReload ?? true;
+            invalidateCommandsLoadCache(directory);
             if (needsReload) {
               requiresReload = true;
               await performFullConfigRefresh({
@@ -384,6 +390,7 @@ export const useCommandsStore = create<CommandsStore>()(
             console.log('[CommandsStore] Command deleted successfully');
 
             const needsReload = payload?.requiresReload ?? true;
+            invalidateCommandsLoadCache(directory);
             if (needsReload) {
               requiresReload = true;
               await performFullConfigRefresh({
@@ -495,6 +502,7 @@ async function performFullConfigRefresh(options: { message?: string; delayMs?: n
 
     const commandsStore = useCommandsStore.getState();
 
+    invalidateCommandsLoadCache();
     await commandsStore.loadCommands();
 
     emitConfigChange("commands", { source: CONFIG_EVENT_SOURCE });
@@ -502,6 +510,7 @@ async function performFullConfigRefresh(options: { message?: string; delayMs?: n
     console.error("[CommandsStore] Failed to refresh configuration after OpenCode restart:", error);
     updateConfigUpdateMessage("OpenCode refresh failed. Please retry refreshing configuration manually.");
     await sleep(1500);
+    throw error;
   } finally {
     finishConfigUpdate();
   }
diff --git a/packages/ui/src/stores/useSkillsCatalogStore.ts b/packages/ui/src/stores/useSkillsCatalogStore.ts
index 9097f905..139348fb 100644
--- a/packages/ui/src/stores/useSkillsCatalogStore.ts
+++ b/packages/ui/src/stores/useSkillsCatalogStore.ts
@@ -13,7 +13,7 @@ import type {
   SkillsCatalogSourceResponse,
 } from '@/lib/api/types';
 
-import { refreshSkillsAfterOpenCodeRestart, useSkillsStore } from '@/stores/useSkillsStore';
+import { invalidateSkillsLoadCache, refreshSkillsAfterOpenCodeRestart, useSkillsStore } from '@/stores/useSkillsStore';
 import { opencodeClient } from '@/lib/opencode/client';
 import { startConfigUpdate, finishConfigUpdate, updateConfigUpdateMessage } from '@/lib/configUpdate';
 import { runtimeFetch } from '@/lib/runtime-fetch';
@@ -423,6 +423,7 @@ export const useSkillsCatalogStore = create<SkillsCatalogState>()(
             });
           } else {
             updateConfigUpdateMessage(payload.message || 'Refreshing skills…');
+            invalidateSkillsLoadCache(currentDirectory);
             void useSkillsStore.getState().loadSkills();
           }
 
diff --git a/packages/ui/src/stores/useSkillsStore.ts b/packages/ui/src/stores/useSkillsStore.ts
index a7c8da91..b59ec55c 100644
--- a/packages/ui/src/stores/useSkillsStore.ts
+++ b/packages/ui/src/stores/useSkillsStore.ts
@@ -168,6 +168,10 @@ const getSkillsCacheKey = (directory: string | null): string => {
   return directory?.trim() || DEFAULT_SKILLS_CACHE_KEY;
 };
 
+export const invalidateSkillsLoadCache = (directory: string | null = getCurrentDirectory()) => {
+  skillsLastLoadedAt.delete(getSkillsCacheKey(directory));
+};
+
 const MAX_HEALTH_WAIT_MS = 20000;
 const FAST_HEALTH_POLL_INTERVAL_MS = 300;
 const FAST_HEALTH_POLL_ATTEMPTS = 4;
@@ -302,6 +306,7 @@ export const useSkillsStore = create<SkillsStore>()(
             }
 
             const needsReload = payload?.requiresReload ?? false;
+            invalidateSkillsLoadCache(currentDirectory);
             if (needsReload) {
               requiresReload = true;
               await refreshSkillsAfterOpenCodeRestart({
@@ -352,6 +357,7 @@ export const useSkillsStore = create<SkillsStore>()(
             }
 
             const needsReload = payload?.requiresReload ?? false;
+            invalidateSkillsLoadCache(currentDirectory);
             if (needsReload) {
               requiresReload = true;
               await refreshSkillsAfterOpenCodeRestart({
@@ -393,6 +399,7 @@ export const useSkillsStore = create<SkillsStore>()(
             }
 
             const needsReload = payload?.requiresReload ?? false;
+            invalidateSkillsLoadCache(currentDirectory);
             if (needsReload) {
               requiresReload = true;
               await refreshSkillsAfterOpenCodeRestart({
@@ -554,13 +561,15 @@ export async function refreshSkillsAfterOpenCodeRestart(options?: { message?: st
     await waitForOpenCodeConnection(options?.delayMs);
     updateConfigUpdateMessage("Refreshing skills…");
     const skillsStore = useSkillsStore.getState();
+    invalidateSkillsLoadCache();
     const loaded = await skillsStore.loadSkills();
     if (loaded) {
       emitConfigChange("skills", { source: CONFIG_EVENT_SOURCE });
     }
-  } catch {
+  } catch (error) {
     updateConfigUpdateMessage("OpenCode refresh failed. Please retry.");
     await sleep(1500);
+    throw error;
   } finally {
     finishConfigUpdate();
   }
diff --git a/packages/vscode/src/opencodeConfig.ts b/packages/vscode/src/opencodeConfig.ts
index 80c79a4b..5b6e28cc 100644
--- a/packages/vscode/src/opencodeConfig.ts
+++ b/packages/vscode/src/opencodeConfig.ts
@@ -1666,6 +1666,39 @@ export const updateAgent = (agentName: string, updates: Record<string, unknown>,
 
   for (const [field, value] of Object.entries(updates || {})) {
     if (field === 'prompt') {
+      if (value === null) {
+        if (mdExists || creatingNewMd) {
+          if (mdData) {
+            mdData.body = '';
+            mdModified = true;
+          }
+          continue;
+        }
+
+        if (isPromptFileReference(jsonSection?.prompt)) {
+          const promptFilePath = resolvePromptFilePath(jsonSection.prompt);
+          if (!promptFilePath) throw new Error(`Invalid prompt file reference for agent ${agentName}`);
+          writePromptFile(promptFilePath, '');
+          continue;
+        }
+
+        if (config.agent) {
+          const agentMap = config.agent as Record<string, unknown>;
+          const current = agentMap[agentName] as Record<string, unknown> | undefined;
+          if (current) {
+            delete current.prompt;
+            if (Object.keys(current).length === 0) {
+              delete agentMap[agentName];
+            }
+            if (Object.keys(agentMap).length === 0) {
+              delete config.agent;
+            }
+            jsonModified = true;
+          }
+        }
+        continue;
+      }
+
       const normalizedValue = typeof value === 'string' ? value : value == null ? '' : String(value);
 
       if (mdExists || creatingNewMd) {
diff --git a/packages/vscode/webview/main.tsx b/packages/vscode/webview/main.tsx
index 1756fe9c..8434d7f6 100644
--- a/packages/vscode/webview/main.tsx
+++ b/packages/vscode/webview/main.tsx
@@ -1354,7 +1354,7 @@ onCommand('showSettings', () => {
 // and refreshes config/data. Triggered by the "Restart API Connection" command.
 onCommand('reloadOpenCode', () => {
   void import('@openchamber/ui/stores/useAgentsStore').then(({ reloadOpenCodeConfiguration }) => {
-    void reloadOpenCodeConfiguration();
+    void reloadOpenCodeConfiguration().catch(() => undefined);
   });
 });
 
diff --git a/packages/web/server/lib/opencode/agents.js b/packages/web/server/lib/opencode/agents.js
index 06932df0..c2a25106 100644
--- a/packages/web/server/lib/opencode/agents.js
+++ b/packages/web/server/lib/opencode/agents.js
@@ -449,6 +449,39 @@ function updateAgent(agentName, updates, workingDirectory) {
 
   for (const [field, value] of Object.entries(updates)) {
     if (field === 'prompt') {
+      if (value === null) {
+        if (mdExists || creatingNewMd) {
+          if (mdData) {
+            mdData.body = '';
+            mdModified = true;
+          }
+          continue;
+        }
+
+        if (isPromptFileReference(jsonSection?.prompt)) {
+          const promptFilePath = resolvePromptFilePath(jsonSection.prompt);
+          if (!promptFilePath) {
+            throw new Error(`Invalid prompt file reference for agent ${agentName}`);
+          }
+          writePromptFile(promptFilePath, '');
+          continue;
+        }
+
+        if (config.agent?.[agentName]) {
+          delete config.agent[agentName].prompt;
+
+          if (Object.keys(config.agent[agentName]).length === 0) {
+            delete config.agent[agentName];
+          }
+          if (Object.keys(config.agent).length === 0) {
+            delete config.agent;
+          }
+
+          jsonModified = true;
+        }
+        continue;
+      }
+
       const normalizedValue = typeof value === 'string' ? value : (value == null ? '' : String(value));
 
       if (mdExists || creatingNewMd) {