diff --git a/strix/config/loader.py b/strix/config/loader.py
index 969d67f8..250790c6 100644
--- a/strix/config/loader.py
+++ b/strix/config/loader.py
@@ -10,11 +10,13 @@ from typing import TYPE_CHECKING, Any
 
 from pydantic import AliasChoices, BaseModel
 
-from strix.config.settings import Settings
+from strix.config.settings import LlmSettings, Settings
 from strix.utils.secret_files import write_secret_text
 
 
 if TYPE_CHECKING:
+    from collections.abc import Mapping
+
     from pydantic.fields import FieldInfo
 
 
@@ -25,6 +27,11 @@ _DEFAULT_PATH: Path = Path.home() / ".strix" / "cli-config.json"
 _override: Path | None = None
 _cached: Settings | None = None
 
+# Model, API key, and API base describe one provider connection. When the shell
+# changes any of them, the stored values of the others no longer belong together
+# and are dropped rather than mixed with the new value.
+_LINKED_LLM_FIELDS = ("model", "api_key", "api_base")
+
 
 def load_settings() -> Settings:
     """Resolve settings from env + JSON file + defaults. Memoized.
@@ -58,13 +65,14 @@ def persist_current() -> None:
 
     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.
+    var set to the empty string clears the field from the file. A change to
+    any linked LLM connection var drops the whole stored connection first.
     """
     s = load_settings()
     target = _override or _DEFAULT_PATH
     target.parent.mkdir(parents=True, exist_ok=True)
 
-    env_block = _read_env_block(target)
+    env_block = _drop_stale_llm_connection(_read_env_block(target))
     for sub_name in type(s).model_fields:
         sub_model = getattr(s, sub_name)
         if not isinstance(sub_model, BaseModel):
@@ -104,7 +112,7 @@ 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.
     """
-    env_block_upper = _read_env_block(path)
+    env_block_upper = _drop_stale_llm_connection(_read_env_block(path))
     if not env_block_upper:
         return {}
     env_present = {k.upper() for k in os.environ}
@@ -128,6 +136,27 @@ def _read_json_overrides(path: Path) -> dict[str, dict[str, Any]]:
     return nested
 
 
+def _first_alias_value(aliases: list[str], source: Mapping[str, Any]) -> Any | None:
+    return next((source[alias] for alias in aliases if alias in source), None)
+
+
+def _drop_stale_llm_connection(env_block: dict[str, Any]) -> dict[str, Any]:
+    """Remove every linked LLM var from ``env_block`` if the shell changed any of them."""
+    linked_aliases = [
+        [alias.upper() for alias in _aliases_for(LlmSettings.model_fields[name])]
+        for name in _LINKED_LLM_FIELDS
+    ]
+    changed = any(
+        (env_value := _first_alias_value(aliases, os.environ)) is not None
+        and env_value != _first_alias_value(aliases, env_block)
+        for aliases in linked_aliases
+    )
+    if not changed:
+        return env_block
+    stale = {alias for aliases in linked_aliases for alias in aliases}
+    return {k: v for k, v in env_block.items() if k not in stale}
+
+
 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():
diff --git a/tests/test_config_loader.py b/tests/test_config_loader.py
index be975f0e..c370f8eb 100644
--- a/tests/test_config_loader.py
+++ b/tests/test_config_loader.py
@@ -229,16 +229,109 @@ def test_persist_current_env_overrides_file_value(
 ) -> None:
     target = tmp_path / "cli-config.json"
     target.write_text(
-        json.dumps({"env": {"STRIX_LLM": "file-model", "LLM_API_KEY": "file-key"}}),
+        json.dumps({"env": {"STRIX_LLM": "file-model", "PERPLEXITY_API_KEY": "file-pplx"}}),
+        encoding="utf-8",
+    )
+    loader.apply_config_override(target)
+    monkeypatch.setenv("PERPLEXITY_API_KEY", "env-pplx")
+
+    loader.persist_current()
+
+    assert json.loads(target.read_text(encoding="utf-8")) == {
+        "env": {"STRIX_LLM": "file-model", "PERPLEXITY_API_KEY": "env-pplx"}
+    }
+
+
+def test_linked_llm_model_change_drops_stored_key_and_base(
+    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",
+                    "LLM_API_BASE": "http://file-base",
+                    "PERPLEXITY_API_KEY": "pplx",
+                }
+            }
+        ),
         encoding="utf-8",
     )
     loader.apply_config_override(target)
     monkeypatch.setenv("STRIX_LLM", "env-model")
 
+    llm = loader.load_settings().llm
+    assert llm.model == "env-model"
+    assert llm.api_key is None
+    assert llm.api_base is None
+
     loader.persist_current()
 
     assert json.loads(target.read_text(encoding="utf-8")) == {
-        "env": {"STRIX_LLM": "env-model", "LLM_API_KEY": "file-key"}
+        "env": {"STRIX_LLM": "env-model", "PERPLEXITY_API_KEY": "pplx"}
+    }
+
+
+def test_linked_llm_key_change_drops_stored_model(
+    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("LLM_API_KEY", "new-key")
+
+    assert loader.load_settings().llm.model is None
+
+    loader.persist_current()
+
+    assert json.loads(target.read_text(encoding="utf-8")) == {"env": {"LLM_API_KEY": "new-key"}}
+
+
+def test_linked_llm_secondary_alias_in_env_is_not_a_change(
+    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("LLM_API_KEY", "file-key")
+    monkeypatch.setenv("OPENAI_API_KEY", "unrelated-global-key")
+
+    llm = loader.load_settings().llm
+    assert llm.model == "file-model"
+    assert llm.api_key == "file-key"
+
+    loader.persist_current()
+
+    assert json.loads(target.read_text(encoding="utf-8")) == {
+        "env": {"STRIX_LLM": "file-model", "LLM_API_KEY": "file-key"}
+    }
+
+
+def test_linked_llm_unchanged_env_keeps_stored_key(
+    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", "file-model")
+
+    assert loader.load_settings().llm.api_key == "file-key"
+
+    loader.persist_current()
+
+    assert json.loads(target.read_text(encoding="utf-8")) == {
+        "env": {"STRIX_LLM": "file-model", "LLM_API_KEY": "file-key"}
     }
 
 
diff --git a/tests/test_dedupe_model.py b/tests/test_dedupe_model.py
index 547f434d..809867b1 100644
--- a/tests/test_dedupe_model.py
+++ b/tests/test_dedupe_model.py
@@ -114,7 +114,14 @@ def test_config_file_loads_dedupe_model(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,
 ) -> None:
-    for key in ("STRIX_LLM", "STRIX_DEDUPE_MODEL", "STRIX_DEDUPE_REASONING_EFFORT"):
+    for key in (
+        "STRIX_LLM",
+        "LLM_API_KEY",
+        "OPENAI_API_KEY",
+        "LLM_API_BASE",
+        "STRIX_DEDUPE_MODEL",
+        "STRIX_DEDUPE_REASONING_EFFORT",
+    ):
         monkeypatch.delenv(key, raising=False)
     path = tmp_path / "config.json"
     path.write_text(