diff --git a/src/cli/config_yaml_edit.c b/src/cli/config_yaml_edit.c
index 38b3b4e33c..a6f8ced105 100644
--- a/src/cli/config_yaml_edit.c
+++ b/src/cli/config_yaml_edit.c
@@ -2698,8 +2698,28 @@ static int yaml_sequence_line_has_unsupported(const yaml_doc_t *doc, const yaml_
     return quote != '\0' ? YAML_MATCH : 0;
 }
 
-static int yaml_sequence_validate_document(const yaml_doc_t *doc) {
-    for (size_t i = 0U; i < doc->line_count; i++) {
+/* Validates only the top-level section the edit descends into. The root
+ * mapping itself was already validated when the document was parsed, so the
+ * section boundaries are sound; every OTHER top-level section is opaque user
+ * content, the same contract the mapping-entry editor applies. Validating the
+ * whole document refused the stock Hermes config for flow sequences such as
+ * `cli: [hermes-cli]` under `platform_toolsets:`, which the hook edit never
+ * reads or rewrites (#2209). An absent root key means the sequence is appended
+ * as a new top-level section, which touches no existing line. */
+static int yaml_sequence_validate_document(const yaml_doc_t *doc, const char *root_key,
+                                           size_t root_key_len) {
+    bool found = false;
+    size_t section_line = 0U;
+    size_t section_colon = 0U;
+    if (yaml_find_unique_key(doc, 0U, root_key, root_key_len, &found, &section_line,
+                             &section_colon) != 0) {
+        return YAML_ERROR;
+    }
+    if (!found) {
+        return 0;
+    }
+    size_t section_end = yaml_top_level_section_end(doc, section_line);
+    for (size_t i = section_line; i < section_end; i++) {
         const yaml_line_t *line = &doc->lines[i];
         if (line->blank || line->comment || line->dquote_cont) {
             continue;
@@ -2947,7 +2967,7 @@ static int yaml_sequence_analyze(const yaml_doc_t *doc, const char *const *seque
                                  const char *identity_key, const char *identity_value,
                                  yaml_mapping_sequence_target_t *target) {
     memset(target, 0, sizeof(*target));
-    if (yaml_sequence_validate_document(doc) != 0) {
+    if (yaml_sequence_validate_document(doc, sequence_path[0], path_lengths[0]) != 0) {
         return YAML_ERROR;
     }
     size_t parent_begin = 0U;
diff --git a/tests/test_config_yaml_edit.c b/tests/test_config_yaml_edit.c
index f6f80d47ea..9efaa2e389 100644
--- a/tests/test_config_yaml_edit.c
+++ b/tests/test_config_yaml_edit.c
@@ -1228,12 +1228,14 @@ TEST(config_yaml_edit_hermes_accepts_interior_brackets_in_plain_scalar_issue1924
 
 TEST(config_yaml_edit_hermes_hook_still_refuses_block_scalar_value_issue1924) {
     /* A `>` or `|` that BEGINS a value is a real block scalar whose
-     * indentation contract this editor does not model: the fail-closed
-     * refusal stays, and the file stays byte-identical. */
+     * indentation contract this editor does not model: inside the `hooks`
+     * subtree the edit descends into, the fail-closed refusal stays and the
+     * file stays byte-identical. The same construct in an untouched section
+     * is opaque user content (#2209). */
     static const char *const initials[] = {
-        "agent:\n  personalities:\n    probe: >\n      folded face\n",
-        "agent:\n  personalities:\n    probe: |\n      literal face\n",
-        "agent:\n  personalities:\n    probe: >-\n      chomped face\n",
+        "hooks:\n  probe: >\n    folded face\n",
+        "hooks:\n  probe: |\n    literal face\n",
+        "hooks:\n  probe: >-\n    chomped face\n",
     };
     for (size_t i = 0U; i < sizeof(initials) / sizeof(initials[0]); i++) {
         yaml_fixture_t fixture;
@@ -1250,10 +1252,10 @@ TEST(config_yaml_edit_hermes_hook_still_refuses_block_scalar_value_issue1924) {
 
 TEST(config_yaml_edit_hermes_hook_still_refuses_nonempty_flow_sequence_value_issue1924) {
     /* Pins the #1631 line: exact `[]` is accepted, a non-empty flow sequence
-     * value is still unsupported in the sequence-document scan. */
-    const char *initial = "agent:\n"
-                          "  personalities:\n"
-                          "    probe: [a, b]\n";
+     * value inside the edited `hooks` subtree is still unsupported. Outside
+     * it, the value is opaque user content (#2209). */
+    const char *initial = "hooks:\n"
+                          "  probe: [a, b]\n";
     yaml_fixture_t fixture;
     ASSERT_EQ(yaml_fixture_init(&fixture, initial), 0);
     ASSERT_EQ(yaml_hermes_hook_upsert(&fixture), CBM_YAML_IDENTITY_EDIT_ERROR);
@@ -2027,6 +2029,57 @@ TEST(config_yaml_edit_remove_on_absent_config_is_a_no_op) {
     PASS();
 }
 
+/* #2209: the stock Hermes config carries flow sequences and block scalars in
+ * sections the hook edit never touches (`platform_toolsets:` -> `cli:
+ * [hermes-cli]`, `plugins:` -> `enabled: [...]`, `|` prompts). They are opaque
+ * user content, exactly as for the mapping-entry editor that writes
+ * `mcp_servers` into the same file; only the `hooks` subtree is validated. */
+TEST(config_yaml_edit_nested_sequence_ignores_foreign_flow_and_block_scalars_issue2209) {
+    const char *initial = "plugins:\n"
+                          "  enabled: [disk-cleanup]\n"
+                          "platform_toolsets:\n"
+                          "  cli: [hermes-cli]\n"
+                          "  telegram: [hermes-telegram]\n"
+                          "toolsets: [all]\n"
+                          "agent:\n"
+                          "  system_prompt: |\n"
+                          "    You are helpful.\n"
+                          "      - keep: [this, text]\n"
+                          "  note: >\n"
+                          "    folded\n"
+                          "model:\n"
+                          "  default: \"anthropic/claude-opus-4.6\"\n";
+    yaml_fixture_t fixture;
+    ASSERT_EQ(yaml_fixture_init(&fixture, initial), 0);
+    ASSERT_EQ(cbm_yaml_upsert_mapping_sequence_item(fixture.path, yaml_hook_sequence_path, 2U, "id",
+                                                    yaml_hook_identity, yaml_hook_canonical_item),
+              CBM_YAML_IDENTITY_EDIT_OK);
+    char *installed = yaml_read_alloc(fixture.path);
+    ASSERT_NOT_NULL(installed);
+    ASSERT_EQ(strncmp(installed, initial, strlen(initial)), 0);
+    ASSERT_NOT_NULL(strstr(installed, "hooks:\n"
+                                      "  pre_llm_call:\n"
+                                      "    - id: \"codebase-memory-mcp\"\n"));
+    ASSERT_EQ(cbm_yaml_upsert_mapping_sequence_item(fixture.path, yaml_hook_sequence_path, 2U, "id",
+                                                    yaml_hook_identity, yaml_hook_canonical_item),
+              CBM_YAML_IDENTITY_EDIT_OK);
+    char *second = yaml_read_alloc(fixture.path);
+    ASSERT_NOT_NULL(second);
+    ASSERT_STR_EQ(second, installed);
+    free(second);
+    free(installed);
+    ASSERT_EQ(cbm_yaml_remove_mapping_sequence_item(fixture.path, yaml_hook_sequence_path, 2U, "id",
+                                                    yaml_hook_identity, yaml_hook_canonical_item),
+              CBM_YAML_IDENTITY_EDIT_OK);
+    char *removed = yaml_read_alloc(fixture.path);
+    ASSERT_NOT_NULL(removed);
+    ASSERT_NULL(strstr(removed, "codebase-memory-mcp"));
+    ASSERT_EQ(strncmp(removed, initial, strlen(initial)), 0);
+    free(removed);
+    th_cleanup(fixture.dir);
+    PASS();
+}
+
 TEST(config_yaml_edit_nested_sequence_ambiguity_fails_byte_identically) {
     const char *cases[] = {
         "hooks:\n   pre_llm_call:\n    - id: \"bad-indent\"\n",
@@ -2192,6 +2245,7 @@ SUITE(config_yaml_edit) {
     RUN_TEST(config_yaml_edit_nested_sequence_preserves_crlf);
     RUN_TEST(config_yaml_edit_nested_sequence_foreign_identity_is_preserved);
     RUN_TEST(config_yaml_edit_nested_sequence_removes_only_exact_canonical_item);
+    RUN_TEST(config_yaml_edit_nested_sequence_ignores_foreign_flow_and_block_scalars_issue2209);
     RUN_TEST(config_yaml_edit_nested_sequence_ambiguity_fails_byte_identically);
     RUN_TEST(config_yaml_edit_remove_on_absent_config_is_a_no_op);
 #ifndef _WIN32