diff --git a/hermes_cli/config.py b/hermes_cli/config.py
index 2e497b12d8e6..a47ba24eaefa 100644
--- a/hermes_cli/config.py
+++ b/hermes_cli/config.py
@@ -5524,10 +5524,13 @@ def _persist_migration(config: Dict[str, Any]) -> None:
 
     Every migration step MUST route its write through this helper instead of
     calling ``save_config`` directly. It is a thin wrapper over
-    ``save_config(config)`` (default-stripping ON); centralising the call makes
-    the invariant impossible to regress one migration at a time. Correctness
-    across seeds, non-default values, behaviour flips, and data transforms is
-    verified by the migration parity tests.
+    ``save_config(config)`` (default-stripping ON, no ``merge_existing``);
+    centralising the call makes the invariant impossible to regress one
+    migration at a time. Callers must pass the full raw config returned by
+    ``read_raw_config()`` after in-place mutations (including key removals);
+    deep-merging the on-disk file back in would resurrect keys the migration
+    just deleted. Partial-save preservation for unrelated top-level sections
+    belongs on ``save_config(..., merge_existing=True)``, not here.
     """
     save_config(config)
 
@@ -6302,6 +6305,25 @@ def migrate_config(interactive: bool = True, quiet: bool = False) -> Dict[str, A
     return results
 
 
+def _merge_partial_save(raw: dict, override: dict) -> dict:
+    """Merge *override* over *raw* for partial ``save_config`` writes.
+
+    Top-level sections omitted from *override* are preserved from *raw*.
+    Shared top-level dict sections are deep-merged so a caller can update one
+    nested key without dropping sibling keys from disk. Intentional key
+    removals within a section are not supported here — migration writes must
+    route through ``_persist_migration`` with a full ``read_raw_config()`` dict
+    instead.
+    """
+    result = copy.deepcopy(override)
+    for key, value in raw.items():
+        if key not in result:
+            result[key] = copy.deepcopy(value)
+        elif isinstance(result.get(key), dict) and isinstance(value, dict):
+            result[key] = _deep_merge(value, result[key])
+    return result
+
+
 def _deep_merge(base: dict, override: dict) -> dict:
     """Recursively merge *override* into *base*, preserving nested defaults.
 
@@ -7184,6 +7206,7 @@ def save_config(
     *,
     strip_defaults: bool = True,
     preserve_keys: Optional[Set[Tuple[str, ...]]] = None,
+    merge_existing: bool = False,
 ):
     """Save configuration to ~/.hermes/config.yaml.\n
 
@@ -7192,6 +7215,12 @@ def save_config(
     before any normalisation).  This prevents config.yaml from being
     contaminated with schema defaults on every save, which makes future
     default changes invisible to users.
+
+    When ``merge_existing`` is True, the on-disk raw config is deep-merged
+    under *config* before writing so partial callers (migration steps via
+    ``_persist_migration``) cannot drop unrelated sections the caller omitted.
+    Full-document replacement callers (dashboard raw YAML editor, callers that
+    already deep-merge) must leave this False so intentional deletions survive.
     """
     with _CONFIG_LOCK:
         if is_managed():
@@ -7226,11 +7255,17 @@ def save_config(
         explicit_raw_paths: Optional[Set[Tuple[str, ...]]] = (
             _explicit_config_paths(_raw_for_paths) if _raw_for_paths else None
         )
+        if merge_existing and _raw_for_paths:
+            config = _merge_partial_save(_raw_for_paths, config)
         # ----------------------------------------------------------------
 
         current_normalized = _normalize_root_model_keys(_normalize_max_turns_config(config))
         normalized = current_normalized
-        raw_existing = _normalize_root_model_keys(_normalize_max_turns_config(read_raw_config()))
+        raw_existing = (
+            _normalize_root_model_keys(_normalize_max_turns_config(_raw_for_paths))
+            if _raw_for_paths
+            else {}
+        )
         if raw_existing:
             normalized = _preserve_env_ref_templates(
                 normalized,
@@ -7278,6 +7313,7 @@ def save_config(
             extra_content="".join(parts) if parts else None,
         )
         _secure_file(config_path)
+        _RAW_CONFIG_CACHE.pop(str(config_path), None)
         _LAST_EXPANDED_CONFIG_BY_PATH[str(config_path)] = copy.deepcopy(current_normalized)
 
 
diff --git a/hermes_cli/web_server.py b/hermes_cli/web_server.py
index 175ab7550e81..406e18f5ca31 100644
--- a/hermes_cli/web_server.py
+++ b/hermes_cli/web_server.py
@@ -14148,7 +14148,9 @@ async def update_config_raw(body: RawConfigUpdate, profile: Optional[str] = None
         if not isinstance(parsed, dict):
             raise HTTPException(status_code=400, detail="YAML must be a mapping")
         with _profile_scope(body.profile or profile):
-            save_config(parsed)
+            # Full-document replacement: the editor owns the whole file; do not
+            # merge omitted sections back from disk (#62723).
+            save_config(parsed, merge_existing=False)
         return {"ok": True}
     except yaml.YAMLError as e:
         raise HTTPException(status_code=400, detail=f"Invalid YAML: {e}")