diff --git a/src/specify_cli/integration_runtime.py b/src/specify_cli/integration_runtime.py
index 9bf8aeac96..98bc6a05b0 100644
--- a/src/specify_cli/integration_runtime.py
+++ b/src/specify_cli/integration_runtime.py
@@ -64,8 +64,15 @@ def with_integration_setting(
     elif raw_options is not None:
         current.pop("parsed_options", None)
 
+    # Recompute the separator from the options actually STORED on ``current``
+    # after the update, not the raw ``parsed_options`` argument. When only
+    # ``script_type`` changes (``parsed_options`` and ``raw_options`` both
+    # None), the previously-stored ``parsed_options`` are retained above, so
+    # deriving the separator from the argument (None) would drop an
+    # options-dependent separator (e.g. Copilot ``--skills`` -> "-") back to
+    # the default ".".
     current["invoke_separator"] = integration.effective_invoke_separator(
-        parsed_options, project_root
+        current.get("parsed_options"), project_root
     )
     settings[key] = current
     return settings
diff --git a/tests/integrations/test_integration_state.py b/tests/integrations/test_integration_state.py
index 1d6bdb0268..fc12d436a4 100644
--- a/tests/integrations/test_integration_state.py
+++ b/tests/integrations/test_integration_state.py
@@ -84,3 +84,31 @@ def test_write_integration_json_strips_integration_key(tmp_path):
     assert state["integration"] == "claude"
     assert state["default_integration"] == "claude"
     assert state["installed_integrations"] == ["claude"]
+
+
+def test_with_integration_setting_recomputes_separator_from_retained_options():
+    """Updating only script_type must not drop an options-dependent separator.
+
+    Copilot resolves the command-ref separator to '-' when '--skills' options
+    are stored and '.' otherwise. A second call that changes only script_type
+    (parsed_options=None, raw_options=None) retains the stored parsed_options,
+    so invoke_separator must stay '-', not be recomputed from the None argument.
+    """
+    from specify_cli.integrations import get_integration
+    from specify_cli.integration_runtime import with_integration_setting
+
+    copilot = get_integration("copilot")
+
+    settings = with_integration_setting(
+        {}, "copilot", copilot, parsed_options={"skills": True}
+    )
+    assert settings["copilot"]["invoke_separator"] == "-"
+
+    settings2 = with_integration_setting(
+        {"integration_settings": settings}, "copilot", copilot, script_type="ps"
+    )
+    # parsed_options are retained (only script_type changed) ...
+    assert settings2["copilot"]["parsed_options"] == {"skills": True}
+    assert settings2["copilot"]["script"] == "ps"
+    # ... so the separator must reflect them, not the (None) argument.
+    assert settings2["copilot"]["invoke_separator"] == "-"