diff --git a/strix/config/loader.py b/strix/config/loader.py
index fbcde898..969d67f8 100644
--- a/strix/config/loader.py
+++ b/strix/config/loader.py
@@ -54,21 +54,32 @@ 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).
+
+    Values already in the file survive when their env var is unset, so a
+    run that gets its settings from the file does not erase them. An env
+    var set to the empty string clears the field from the file.
+    """
     s = load_settings()
     target = _override or _DEFAULT_PATH
     target.parent.mkdir(parents=True, exist_ok=True)
 
-    env_block: dict[str, str] = {}
-    for sub_name in s.model_fields:
+    env_block = _read_env_block(target)
+    for sub_name in type(s).model_fields:
         sub_model = getattr(s, sub_name)
         if not isinstance(sub_model, BaseModel):
             continue
         for finfo in type(sub_model).model_fields.values():
-            for alias in _aliases_for(finfo):
-                value = os.environ.get(alias.upper())
+            aliases = [alias.upper() for alias in _aliases_for(finfo)]
+            set_aliases = [alias for alias in aliases if os.environ.get(alias) is not None]
+            if not set_aliases:
+                continue
+            for alias in aliases:
+                env_block.pop(alias, None)
+            for alias in set_aliases:
+                value = os.environ[alias]
                 if value:
-                    env_block[alias.upper()] = value
+                    env_block[alias] = value
                     break
 
     write_secret_text(target, json.dumps({"env": env_block}, indent=2))
@@ -93,17 +104,9 @@ def _read_json_overrides(path: Path) -> dict[str, dict[str, Any]]:
     Only includes keys whose env var is NOT already set, so env always
     wins over the persisted file.
     """
-    if not path.exists():
+    env_block_upper = _read_env_block(path)
+    if not env_block_upper:
         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 {}
-
-    env_block_upper = {str(k).upper(): v for k, v in env_block.items()}
     env_present = {k.upper() for k in os.environ}
 
     nested: dict[str, dict[str, Any]] = {}
@@ -123,3 +126,17 @@ def _read_json_overrides(path: Path) -> dict[str, dict[str, Any]]:
         if sub_data:
             nested[sub_name] = sub_data
     return nested
+
+
+def _read_env_block(path: Path) -> dict[str, Any]:
+    """Return the ``env`` block stored in ``path`` with upper-cased keys, or ``{}``."""
+    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(k).upper(): v for k, v in env_block.items()}
diff --git a/tests/test_config_loader.py b/tests/test_config_loader.py
index e83ab119..be975f0e 100644
--- a/tests/test_config_loader.py
+++ b/tests/test_config_loader.py
@@ -208,6 +208,82 @@ def test_persist_current_writes_env_block(tmp_path: Path, monkeypatch: pytest.Mo
     }
 
 
+def test_persist_current_keeps_file_values_when_env_is_unset(tmp_path: Path) -> None:
+    target = tmp_path / "cli-config.json"
+    target.write_text(
+        json.dumps({"env": {"STRIX_LLM": "file-model", "LLM_API_KEY": "file-key"}}),
+        encoding="utf-8",
+    )
+    loader.apply_config_override(target)
+    assert loader.load_settings().llm.model == "file-model"
+
+    loader.persist_current()
+
+    assert json.loads(target.read_text(encoding="utf-8")) == {
+        "env": {"STRIX_LLM": "file-model", "LLM_API_KEY": "file-key"}
+    }
+
+
+def test_persist_current_env_overrides_file_value(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    target = tmp_path / "cli-config.json"
+    target.write_text(
+        json.dumps({"env": {"STRIX_LLM": "file-model", "LLM_API_KEY": "file-key"}}),
+        encoding="utf-8",
+    )
+    loader.apply_config_override(target)
+    monkeypatch.setenv("STRIX_LLM", "env-model")
+
+    loader.persist_current()
+
+    assert json.loads(target.read_text(encoding="utf-8")) == {
+        "env": {"STRIX_LLM": "env-model", "LLM_API_KEY": "file-key"}
+    }
+
+
+def test_persist_current_env_alias_replaces_other_alias_in_file(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    target = tmp_path / "cli-config.json"
+    target.write_text(json.dumps({"env": {"OPENAI_API_KEY": "old-key"}}), encoding="utf-8")
+    loader.apply_config_override(target)
+    monkeypatch.setenv("LLM_API_KEY", "new-key")
+
+    loader.persist_current()
+
+    assert json.loads(target.read_text(encoding="utf-8")) == {"env": {"LLM_API_KEY": "new-key"}}
+
+
+def test_persist_current_empty_env_clears_file_value(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    target = tmp_path / "cli-config.json"
+    target.write_text(
+        json.dumps({"env": {"STRIX_LLM": "file-model", "PERPLEXITY_API_KEY": "pplx"}}),
+        encoding="utf-8",
+    )
+    loader.apply_config_override(target)
+    monkeypatch.setenv("PERPLEXITY_API_KEY", "")
+
+    loader.persist_current()
+
+    assert json.loads(target.read_text(encoding="utf-8")) == {"env": {"STRIX_LLM": "file-model"}}
+
+
+def test_persist_current_replaces_corrupt_file(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    target = tmp_path / "cli-config.json"
+    target.write_text("{not json", encoding="utf-8")
+    loader.apply_config_override(target)
+    monkeypatch.setenv("STRIX_LLM", "env-model")
+
+    loader.persist_current()
+
+    assert json.loads(target.read_text(encoding="utf-8")) == {"env": {"STRIX_LLM": "env-model"}}
+
+
 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"