diff --git a/hermes_cli/config.py b/hermes_cli/config.py
index 595b0e1576e..1034816f2e8 100644
--- a/hermes_cli/config.py
+++ b/hermes_cli/config.py
@@ -4827,7 +4827,7 @@ def migrate_config(interactive: bool = True, quiet: bool = False) -> Dict[str, A
     
     # ── Version 3 → 4: migrate tool progress from .env to config.yaml ──
     if current_ver < 4:
-        config = load_config()
+        config = read_raw_config()
         display = config.get("display", {})
         if not isinstance(display, dict):
             display = {}
@@ -4850,7 +4850,7 @@ def migrate_config(interactive: bool = True, quiet: bool = False) -> Dict[str, A
     
     # ── Version 4 → 5: add timezone field ──
     if current_ver < 5:
-        config = load_config()
+        config = read_raw_config()
         if "timezone" not in config:
             old_tz = os.getenv("HERMES_TIMEZONE", "")
             if old_tz and old_tz.strip():
@@ -4878,7 +4878,7 @@ def migrate_config(interactive: bool = True, quiet: bool = False) -> Dict[str, A
 
     # ── Version 11 → 12: migrate custom_providers list → providers dict ──
     if current_ver < 12:
-        config = load_config()
+        config = read_raw_config()
         custom_list = config.get("custom_providers")
         if isinstance(custom_list, list) and custom_list:
             providers_dict = config.get("providers", {})
@@ -4969,7 +4969,7 @@ def migrate_config(interactive: bool = True, quiet: bool = False) -> Dict[str, A
         if isinstance(raw_stt, dict) and "model" in raw_stt:
             legacy_model = raw_stt["model"]
             provider = raw_stt.get("provider", "local")
-            config = load_config()
+            config = read_raw_config()
             stt = config.get("stt", {})
             # Remove the legacy flat key
             stt.pop("model", None)
@@ -5434,7 +5434,7 @@ def migrate_config(interactive: bool = True, quiet: bool = False) -> Dict[str, A
     missing_config = get_missing_config_fields()
     
     if missing_config:
-        config = load_config()
+        config = read_raw_config()
         
         for field in missing_config:
             key = field["key"]
@@ -5450,7 +5450,7 @@ def migrate_config(interactive: bool = True, quiet: bool = False) -> Dict[str, A
         save_config(config)
     elif current_ver < latest_ver:
         # Just update version
-        config = load_config()
+        config = read_raw_config()
         config["_config_version"] = latest_ver
         save_config(config)
 
@@ -5472,7 +5472,7 @@ def migrate_config(interactive: bool = True, quiet: bool = False) -> Dict[str, A
 
         if answer in {"y", "yes"}:
             print()
-            config = load_config()
+            config = read_raw_config()
             try:
                 from agent.skill_utils import SKILL_CONFIG_PREFIX
             except Exception:
diff --git a/tests/hermes_cli/test_config.py b/tests/hermes_cli/test_config.py
index 7e938836b81..17995d1fd9a 100644
--- a/tests/hermes_cli/test_config.py
+++ b/tests/hermes_cli/test_config.py
@@ -1062,7 +1062,7 @@ class TestDiscordChannelPromptsConfig:
     def test_default_config_includes_discord_channel_prompts(self):
         assert DEFAULT_CONFIG["discord"]["channel_prompts"] == {}
 
-    def test_migrate_adds_discord_channel_prompts_default(self, tmp_path):
+    def test_migrate_does_not_expand_discord_channel_prompts_default(self, tmp_path):
         config_path = tmp_path / "config.yaml"
         config_path.write_text(
             yaml.safe_dump({"_config_version": 17, "discord": {"auto_thread": True}}),
@@ -1076,7 +1076,50 @@ class TestDiscordChannelPromptsConfig:
         from hermes_cli.config import DEFAULT_CONFIG
         assert raw["_config_version"] == DEFAULT_CONFIG["_config_version"]
         assert raw["discord"]["auto_thread"] is True
-        assert raw["discord"]["channel_prompts"] == {}
+        # channel_prompts is a DEFAULT_CONFIG value that should NOT be expanded
+        # into the user's file — read_raw_config() preserves only what the user
+        # explicitly wrote (fixes #40821: config migration expanding defaults).
+        assert "channel_prompts" not in raw.get("discord", {})
+
+    def test_migrate_preserves_custom_providers_and_no_defaults_dump(self, tmp_path):
+        """Migration must not expand config.yaml to a defaults dump (#40821).
+
+        Before the fix, migrations used load_config() which deep-merges
+        DEFAULT_CONFIG, then save_config() wrote the full ~13KB expanded
+        result — destroying comments and structure. Using read_raw_config()
+        keeps the file small and preserves only the user's actual config.
+        """
+        config_path = tmp_path / "config.yaml"
+        config_path.write_text(
+            yaml.safe_dump({
+                "_config_version": 3,
+                "model": {"default": "test-model", "provider": "openrouter"},
+                "custom_providers": [
+                    {"name": "local-llm", "base_url": "http://localhost:8080/v1",
+                     "models": {"test": {}}}
+                ],
+            }),
+            encoding="utf-8",
+        )
+
+        with patch.dict(os.environ, {"HERMES_HOME": str(tmp_path)}):
+            migrate_config(interactive=False, quiet=True)
+            raw = yaml.safe_load(config_path.read_text(encoding="utf-8"))
+
+        # custom_providers migrated to providers dict (by design, v11->v12)
+        assert "custom_providers" not in raw
+        assert "providers" in raw
+        assert "local-llm" in raw["providers"]
+        assert raw["providers"]["local-llm"]["api"] == "http://localhost:8080/v1"
+
+        # File must NOT be a defaults dump — assert specific DEFAULT_CONFIG
+        # top-level keys are absent (they should only appear via load_config's
+        # deep-merge, not be written to the user's file by migration).
+        for default_key in ("tts", "compression", "security", "whatsapp", "bedrock"):
+            assert default_key not in raw, (
+                f"{default_key} should not be in migrated config file — "
+                f"migration should use read_raw_config() to avoid defaults dump"
+            )
 
 
 class TestUserMessagePreviewConfig: