diff --git a/server/src/routes/agents.ts b/server/src/routes/agents.ts
index 2ad85e63..c2cacfe4 100644
--- a/server/src/routes/agents.ts
+++ b/server/src/routes/agents.ts
@@ -1772,6 +1772,18 @@ export function agentRoutes(db: Db) {
         rawEffectiveAdapterConfig = { ...existingAdapterConfig, ...requestedAdapterConfig };
       }
       if (changingAdapterType) {
+        // Preserve adapter-agnostic keys (env, cwd, etc.) from the existing config
+        // when the adapter type changes. Without this, a PATCH that includes
+        // adapterConfig but omits these keys would silently drop them.
+        const ADAPTER_AGNOSTIC_KEYS = [
+          "env", "cwd", "timeoutSec", "graceSec",
+          "promptTemplate", "bootstrapPromptTemplate",
+        ] as const;
+        for (const key of ADAPTER_AGNOSTIC_KEYS) {
+          if (rawEffectiveAdapterConfig[key] === undefined && existingAdapterConfig[key] !== undefined) {
+            rawEffectiveAdapterConfig = { ...rawEffectiveAdapterConfig, [key]: existingAdapterConfig[key] };
+          }
+        }
         rawEffectiveAdapterConfig = preserveInstructionsBundleConfig(
           existingAdapterConfig,
           rawEffectiveAdapterConfig,
diff --git a/ui/src/components/AgentConfigForm.tsx b/ui/src/components/AgentConfigForm.tsx
index 06c74e65..c3c9bdfa 100644
--- a/ui/src/components/AgentConfigForm.tsx
+++ b/ui/src/components/AgentConfigForm.tsx
@@ -1155,9 +1155,17 @@ function EnvVarEditor({
   const [rows, setRows] = useState<Row[]>(() => toRows(value));
   const [sealError, setSealError] = useState<string | null>(null);
   const valueRef = useRef(value);
+  const emittingRef = useRef(false);
 
-  // Sync when value identity changes (overlay reset after save)
+  // Sync when value identity changes (overlay reset after save).
+  // Skip re-sync when the change was triggered by our own emit() to avoid
+  // reverting local row state (e.g. a secret-transition dropdown choice).
   useEffect(() => {
+    if (emittingRef.current) {
+      emittingRef.current = false;
+      valueRef.current = value;
+      return;
+    }
     if (value !== valueRef.current) {
       valueRef.current = value;
       setRows(toRows(value));
@@ -1170,12 +1178,18 @@ function EnvVarEditor({
       const k = row.key.trim();
       if (!k) continue;
       if (row.source === "secret") {
-        if (!row.secretId) continue;
-        rec[k] = { type: "secret_ref", secretId: row.secretId, version: "latest" };
+        if (row.secretId) {
+          rec[k] = { type: "secret_ref", secretId: row.secretId, version: "latest" };
+        } else {
+          // Row is transitioning to secret but user hasn't picked one yet.
+          // Preserve the plain value so it isn't silently dropped.
+          rec[k] = { type: "plain", value: row.plainValue };
+        }
       } else {
         rec[k] = { type: "plain", value: row.plainValue };
       }
     }
+    emittingRef.current = true;
     onChange(Object.keys(rec).length > 0 ? rec : undefined);
   }