diff --git a/cli-config.yaml.example b/cli-config.yaml.example
index 21ff9ea6e4..a622c100fd 100644
--- a/cli-config.yaml.example
+++ b/cli-config.yaml.example
@@ -4,6 +4,11 @@
 # This file configures CLI behavior; only documented secret environment
 # variables in .env take precedence over their corresponding settings.
 
+# Schema version of this file. The installers copy it to seed config.yaml, and
+# `hermes update` uses it to know which one-time migrations the file already
+# has. Hermes manages it: do not copy it into another config.
+_config_version: 46
+
 # =============================================================================
 # Database Configuration
 # =============================================================================
diff --git a/hermes_cli/config.py b/hermes_cli/config.py
index ca846e01b7..9f6038fdd7 100644
--- a/hermes_cli/config.py
+++ b/hermes_cli/config.py
@@ -1310,17 +1310,14 @@ def migrate_config(interactive: bool = True, quiet: bool = False) -> Dict[str, A
 
     # Auto-migration support floor (v12): an EXPLICIT on-disk ``_config_version`` below the
     # floor is NOT migrated and NOT rewritten — surface a message and leave the file untouched
-    # (deep-merge supplies defaults at read time). A config with NO version key is a fresh
-    # minimal config, not an ancient install: it gets the normal ladder and a version stamp.
+    # (deep-merge supplies defaults at read time). A config with NO version key is not an
+    # ancient install: it gets only the legacy-key steps and a version stamp.
     # Missing/unparseable files never trip the floor gate.
     # Imported lazily because the steps call back into this module.
     from hermes_cli.config_migrations import (
-        SUPPORT_FLOOR_VERSION, run_migrations, support_floor_message)
+        SUPPORT_FLOOR_VERSION, has_version_stamp, run_migrations, support_floor_message)
 
-    try:
-        has_explicit_version = "_config_version" in read_user_config_raw()
-    except Exception:
-        has_explicit_version = False
+    has_explicit_version = has_version_stamp()
     floor_refused = (
         has_explicit_version and current_ver < SUPPORT_FLOOR_VERSION and current_ver < latest_ver)
     if floor_refused:
@@ -1331,7 +1328,7 @@ def migrate_config(interactive: bool = True, quiet: bool = False) -> Dict[str, A
         if not quiet:
             print(f"  ⚠ {msg}")
     else:
-        run_migrations(current_ver, results, quiet)
+        run_migrations(current_ver, results, quiet, unversioned=not has_explicit_version)
 
     _disable_suspicious_mcp_servers(results, quiet)
     _warn_invalid_platform_toolsets(results, quiet)
diff --git a/hermes_cli/config_migrations.py b/hermes_cli/config_migrations.py
index b011814ea2..a4f1eff099 100644
--- a/hermes_cli/config_migrations.py
+++ b/hermes_cli/config_migrations.py
@@ -36,6 +36,16 @@ def support_floor_message() -> str:
         "after reviewing the changelog.")
 
 
+def has_version_stamp() -> bool:
+    """Whether config.yaml carries a ``_config_version`` key. ``check_config_version()`` reads a
+    missing one as 0, but such a file is never-stamped current-schema content, not an ancient
+    install: the floor must not refuse it and only :data:`LEGACY_KEY_STEPS` may run on it."""
+    try:
+        return "_config_version" in _cfg().read_user_config_raw()
+    except Exception:
+        return False
+
+
 def _cfg():
     """Return the live ``hermes_cli.config`` module (lazy, cycle-free, monkeypatch-friendly)."""
     from hermes_cli import config
@@ -755,15 +765,26 @@ MIGRATIONS: Tuple[Tuple[int, Callable[[Dict[str, Any], bool], None]], ...] = (
     (46, _migrate_to_46),
 )
 
+#: Steps triggered by a legacy key or identifier (a renamed or retired key, a removed plugin or
+#: toolset, the plugin-era SOUL.md section): they carry its setting to where the runtime reads it
+#: or drop what nothing reads, which is right however old the file is. A config.yaml with no
+#: ``_config_version`` is current-schema content that was never stamped (installers seed it from
+#: cli-config.yaml.example; targeted writers never stamp), so it gets only these: every other step
+#: decides by a value or an absence that, in such a file, is the user's own choice. v13 is left
+#: out: it clears OPENAI_MODEL from .env, a generic name Hermes never reads but the user's tools may.
+LEGACY_KEY_STEPS = frozenset({12, 14, 16, 17, 29, 33, 38, 39, 41, 42, 43, 46})
 
-def run_migrations(current_ver: int, results: Dict[str, Any], quiet: bool) -> None:
-    """Apply every registered migration whose target version exceeds *current_ver*.
+
+def run_migrations(
+    current_ver: int, results: Dict[str, Any], quiet: bool, *, unversioned: bool = False) -> None:
+    """Apply every registered migration whose target version exceeds *current_ver*; a config
+    with no ``_config_version`` (*unversioned*) gets only :data:`LEGACY_KEY_STEPS`.
 
     *current_ver* is the on-disk schema version captured ONCE before any step runs and does not
     advance between steps — each step is gated on the same initial value.
     """
     for target_ver, migration_fn in MIGRATIONS:
-        if current_ver < target_ver:
+        if current_ver < target_ver and (target_ver in LEGACY_KEY_STEPS or not unversioned):
             try:
                 migration_fn(results, quiet)
             except Exception as exc:
diff --git a/scripts/docker_config_migrate.py b/scripts/docker_config_migrate.py
index 2e9d3d66b1..cede0d4b9f 100644
--- a/scripts/docker_config_migrate.py
+++ b/scripts/docker_config_migrate.py
@@ -16,6 +16,7 @@ from hermes_cli.config import (
 from hermes_cli.config_backups import backup_config, list_config_backups
 from hermes_cli.config_migrations import (
     SUPPORT_FLOOR_VERSION,
+    has_version_stamp,
     support_floor_message,
 )
 from utils import env_var_enabled
@@ -54,8 +55,10 @@ def main() -> int:
     # Below the auto-migration support floor: migrate_config() refuses (and
     # leaves the file untouched), so don't run the backup/verify dance that
     # would raise "did not advance config version" and block the boot.
-    # Warn-and-continue matches the CLI's fail-safe posture.
-    if current_ver < SUPPORT_FLOOR_VERSION:
+    # Warn-and-continue matches the CLI's fail-safe posture. A config with no
+    # _config_version (a volume seeded from the template) is not below the
+    # floor: migrate_config() stamps it.
+    if current_ver < SUPPORT_FLOOR_VERSION and has_version_stamp():
         print(
             f"[config-migrate] WARNING: {support_floor_message()}",
             file=sys.stderr,
diff --git a/tests/hermes_cli/test_config_unversioned_migration.py b/tests/hermes_cli/test_config_unversioned_migration.py
new file mode 100644
index 0000000000..6b22b3d6d0
--- /dev/null
+++ b/tests/hermes_cli/test_config_unversioned_migration.py
@@ -0,0 +1,78 @@
+"""A config.yaml without ``_config_version`` is current-schema content that was never stamped:
+the installers seed it from cli-config.yaml.example and targeted writers (``hermes config set``,
+/personality) never stamp. The one-time migration ladder must not treat it as a v0 install —
+its value- and absence-based steps would overwrite what the user chose."""
+
+import shutil
+from pathlib import Path
+
+import pytest
+import yaml
+
+TEMPLATE = Path(__file__).resolve().parents[2] / "cli-config.yaml.example"
+
+USER_CHOICES = {
+    "delegation.max_concurrent_children": "3",
+    "delegation.max_iterations": "50",
+    "display.background_process_notifications": "all",
+    "agent.verify_on_stop": "true",
+    "curator.stale_after_days": "30",
+    "curator.archive_after_days": "90",
+    "model_catalog.ttl_hours": "24",
+}
+WATCHED = [*USER_CHOICES, "display.personality", "plugins.enabled"]
+
+
+@pytest.fixture
+def hermes_home(tmp_path, monkeypatch):
+    home = tmp_path / ".hermes"
+    home.mkdir()
+    monkeypatch.setattr(Path, "home", lambda: tmp_path)  # sibling-profile scan stays in tmp
+    monkeypatch.setenv("HERMES_HOME", str(home))
+    return home
+
+
+def _raw(home: Path) -> dict:
+    return yaml.safe_load((home / "config.yaml").read_text(encoding="utf-8")) or {}
+
+
+def _at(raw: dict, dotted: str):
+    for part in dotted.split("."):
+        raw = raw.get(part) if isinstance(raw, dict) else None
+    return raw
+
+
+def test_update_keeps_user_values_of_an_unversioned_config_and_migrates_legacy_keys(hermes_home):
+    from hermes_cli.config import DEFAULT_CONFIG, set_config_value
+    from hermes_cli.personality import persist_personality
+    from hermes_cli.update_cmd import _check_and_apply_config_migration
+
+    # Seeded before the template carried a stamp; early-2026 templates shipped this retired key.
+    (hermes_home / "config.yaml").write_text(
+        "compression:\n  summary_model: google/gemini-3-flash-preview\n", encoding="utf-8")
+    # Installed with `hermes plugins install` and never enabled.
+    plugin = hermes_home / "plugins" / "notes-helper"
+    plugin.mkdir(parents=True)
+    (plugin / "plugin.yaml").write_text("name: notes-helper\nversion: 0.1.0\n", encoding="utf-8")
+    assert persist_personality("kawaii")
+    for key, value in USER_CHOICES.items():
+        set_config_value(key, value)
+    before = _raw(hermes_home)
+
+    _check_and_apply_config_migration()
+
+    after = _raw(hermes_home)
+    assert {k: _at(after, k) for k in WATCHED} == {k: _at(before, k) for k in WATCHED}
+    assert "summary_model" not in after["compression"]
+    assert _at(after, "auxiliary.compression.model") == _at(before, "compression.summary_model")
+    assert after["_config_version"] == DEFAULT_CONFIG["_config_version"]
+
+
+def test_config_seeded_from_the_template_reads_as_current(hermes_home):
+    """install.sh, install.ps1, docker/stage2-hook.sh and `hermes doctor --fix` copy the template."""
+    from hermes_cli.config import check_config_version
+
+    shutil.copy(TEMPLATE, hermes_home / "config.yaml")
+
+    current, latest = check_config_version(raise_on_parse_error=True)
+    assert current == latest
diff --git a/tests/tools/test_docker_config_migrate.py b/tests/tools/test_docker_config_migrate.py
index ac9d3040be..dbdd4ef2b7 100644
--- a/tests/tools/test_docker_config_migrate.py
+++ b/tests/tools/test_docker_config_migrate.py
@@ -101,19 +101,20 @@ def test_docker_config_migrate_skips_below_floor_config_untouched(tmp_path: Path
     assert not list(tmp_path.glob("*.bak-*"))
 
 
-def test_docker_config_migrate_skips_unversioned_config_untouched(tmp_path: Path) -> None:
-    """Unversioned configs coerce to version 0 — below the floor, so refused."""
+def test_docker_config_migrate_stamps_unversioned_config(tmp_path: Path) -> None:
+    """A config with no _config_version (a template-seeded volume) is not below the floor, as in
+    migrate_config(): it is stamped and keeps its values."""
     config_path = tmp_path / "config.yaml"
-    original = yaml.safe_dump({"model": {"default": "m", "provider": "openrouter"}})
-    config_path.write_text(original, encoding="utf-8")
+    model = {"default": "m", "provider": "openrouter"}
+    config_path.write_text(yaml.safe_dump({"model": model}), encoding="utf-8")
 
     proc = _run_migration(tmp_path)
 
     assert proc.returncode == 0, proc.stderr
-    assert "Migrating config schema" not in proc.stdout
-    assert "can no longer be auto-migrated" in proc.stderr
-    assert config_path.read_text(encoding="utf-8") == original
-    assert not list(tmp_path.glob("*.bak-*"))
+    assert "can no longer be auto-migrated" not in proc.stderr
+    raw = yaml.safe_load(config_path.read_text(encoding="utf-8"))
+    assert raw["_config_version"] == DEFAULT_CONFIG["_config_version"]
+    assert raw["model"] == model
 
 
 def test_docker_config_migrate_does_not_rewrite_invalid_yaml(tmp_path: Path) -> None: