diff --git a/strix/config/loader.py b/strix/config/loader.py
index fbcde898..03c59ea0 100644
--- a/strix/config/loader.py
+++ b/strix/config/loader.py
@@ -54,12 +54,16 @@ def apply_config_override(path: Path) -> None:
 
 
 def persist_current() -> None:
-    """Write currently-set env vars to the active config file (0o600)."""
+    """Merge currently-set env vars into the active config file (0o600).
+
+    Keys already on disk are preserved (including keys unknown to this
+    version's schema); env vars win on conflicts.
+    """
     s = load_settings()
     target = _override or _DEFAULT_PATH
     target.parent.mkdir(parents=True, exist_ok=True)
 
-    env_block: dict[str, str] = {}
+    env_block: dict[str, Any] = _read_persisted_env(target)
     for sub_name in s.model_fields:
         sub_model = getattr(s, sub_name)
         if not isinstance(sub_model, BaseModel):
@@ -74,6 +78,24 @@ def persist_current() -> None:
     write_secret_text(target, json.dumps({"env": env_block}, indent=2))
 
 
+def _read_persisted_env(path: Path) -> dict[str, Any]:
+    """Read the ``{"env": {...}}`` block already stored at ``path``."""
+    if not path.exists():
+        return {}
+    try:
+        data = json.loads(path.read_text(encoding="utf-8"))
+    except (json.JSONDecodeError, OSError):
+        return {}
+    env_block = data.get("env", {}) if isinstance(data, dict) else {}
+    if not isinstance(env_block, dict):
+        return {}
+    return {
+        str(key).upper(): value
+        for key, value in env_block.items()
+        if value is not None and value != ""
+    }
+
+
 def _aliases_for(finfo: FieldInfo) -> list[str]:
     """Collect every env-var name that should populate ``finfo``."""
     aliases: list[str] = []
diff --git a/tests/test_config_loader.py b/tests/test_config_loader.py
index e83ab119..5b70fc5d 100644
--- a/tests/test_config_loader.py
+++ b/tests/test_config_loader.py
@@ -208,6 +208,69 @@ def test_persist_current_writes_env_block(tmp_path: Path, monkeypatch: pytest.Mo
     }
 
 
+def test_persist_current_preserves_keys_missing_from_env(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    monkeypatch.delenv("STRIX_LLM", raising=False)
+    monkeypatch.delenv("LLM_API_KEY", raising=False)
+    monkeypatch.setenv("OPENAI_API_KEY", "env-key")
+    target = tmp_path / "cli-config.json"
+    target.write_text(
+        json.dumps({"env": {"STRIX_LLM": "file-model", "STRIX_FUTURE_KEY": "keep-me"}}),
+        encoding="utf-8",
+    )
+    loader.apply_config_override(target)
+
+    loader.persist_current()
+
+    assert json.loads(target.read_text(encoding="utf-8")) == {
+        "env": {
+            "STRIX_LLM": "file-model",
+            "STRIX_FUTURE_KEY": "keep-me",
+            "OPENAI_API_KEY": "env-key",
+        }
+    }
+
+
+def test_persist_current_env_wins_over_persisted_value(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    monkeypatch.setenv("STRIX_LLM", "env-model")
+    target = tmp_path / "cli-config.json"
+    target.write_text(json.dumps({"env": {"STRIX_LLM": "file-model"}}), encoding="utf-8")
+    loader.apply_config_override(target)
+
+    loader.persist_current()
+
+    assert json.loads(target.read_text(encoding="utf-8"))["env"]["STRIX_LLM"] == "env-model"
+
+
+def test_persist_current_preserves_dict_valued_key(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    monkeypatch.delenv("STRIX_LLM", raising=False)
+    monkeypatch.delenv("LLM_EXTRA_HEADERS", raising=False)
+    target = tmp_path / "cli-config.json"
+    target.write_text(
+        json.dumps(
+            {
+                "env": {
+                    "STRIX_LLM": "file-model",
+                    "LLM_EXTRA_HEADERS": {"X-Foo": "bar"},
+                }
+            }
+        ),
+        encoding="utf-8",
+    )
+    loader.apply_config_override(target)
+
+    loader.persist_current()
+
+    persisted_env = json.loads(target.read_text(encoding="utf-8"))["env"]
+    assert persisted_env["STRIX_LLM"] == "file-model"
+    assert persisted_env["LLM_EXTRA_HEADERS"] == {"X-Foo": "bar"}
+
+
 def test_persist_current_sets_0600_mode(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
     monkeypatch.setenv("STRIX_LLM", "persisted-model")
     target = tmp_path / "cli-config.json"