diff --git a/README.md b/README.md
index 55be0c9cac..355df27cd2 100644
--- a/README.md
+++ b/README.md
@@ -201,7 +201,8 @@ streams simulate chunks from a non-streaming response, while no-tool streams sta
    values override shell exports, and a project-root override alone still uses
    `backend/.deer-flow` first. Simple variable references such as
    `DEER_FLOW_HOME="$PWD/backend/.deer-flow"` use the checkout as `PWD`;
-   single-quoted references remain literal. For standalone Gateway launches using `backend/.env`
+   single-quoted references remain literal. If the checkout `.env` cannot be read or decoded
+   as UTF-8, thread diagnostics retain shell exports and default storage paths. For standalone Gateway launches using `backend/.env`
    or `DEER_FLOW_ENV_FILE`, export the effective `DEER_FLOW_HOME` when collecting
    the bundle and ensure the checkout `.env` does not override it.
    Doctor's internal tool probes also decode UTF-8 with replacement for invalid
diff --git a/backend/tests/test_support_bundle.py b/backend/tests/test_support_bundle.py
index f6af247e70..fa5f3240ef 100644
--- a/backend/tests/test_support_bundle.py
+++ b/backend/tests/test_support_bundle.py
@@ -25,6 +25,32 @@ def _zip_text(zip_path, name: str) -> str:
         return zf.read(name).decode("utf-8")
 
 
+@pytest.mark.parametrize("failure", ["permission", "encoding"])
+@pytest.mark.parametrize("configured_home", [False, True])
+def test_unreadable_dotenv_keeps_thread_diagnostics(tmp_path, monkeypatch, failure, configured_home):
+    project = tmp_path / "checkout"
+    project.mkdir()
+    home = tmp_path / "data" if configured_home else project / ".deer-flow"
+    (home / "threads" / "broken-env" / "user-data").mkdir(parents=True)
+    env_file = project / ".env"
+    # A valid prefix must not partially change runtime paths when decoding fails.
+    env_file.write_bytes(b"DEER_FLOW_HOME=wrong-home\n" + b"#" * 10000 + b"\xff")
+    if configured_home:
+        monkeypatch.setenv("DEER_FLOW_HOME", str(home))
+    if failure == "permission":
+        original_open = Path.open
+
+        def guarded_open(path, *args, **kwargs):
+            if path == env_file:
+                raise PermissionError("Cannot read .env")
+            return original_open(path, *args, **kwargs)
+
+        monkeypatch.setattr(Path, "open", guarded_open)
+
+    summary = support_bundle.collect_thread_summary(project, "broken-env")
+    assert summary["found"] is True
+
+
 @pytest.mark.parametrize("layout", ["threads/thread-home", "users/alice/threads/thread-home"])
 def test_thread_summary_uses_configured_runtime_home(tmp_path, monkeypatch, layout):
     project = tmp_path / "checkout"
diff --git a/scripts/AGENTS.md b/scripts/AGENTS.md
index 827ae60e39..1d7117cec9 100644
--- a/scripts/AGENTS.md
+++ b/scripts/AGENTS.md
@@ -4,7 +4,9 @@ Thread manifests use a nonempty `DEER_FLOW_HOME` exclusively, resolving relative
 values from the checkout like the local launcher. Read root `.env` path settings
 without exporting secrets; dotenv overrides shell exports, including empty values.
 Expand unquoted leading tildes, preserving quoted literals. If python-dotenv is
-unavailable, retain shell/legacy lookup so troubleshooting remains usable.
+unavailable or `.env` cannot be read/decoded as UTF-8, retain shell/legacy lookup
+so troubleshooting remains usable. Read the complete file before applying any
+assignments so a decoding failure cannot partially override shell values.
 Resolve `$NAME`, `${NAME}` and `${NAME:-literal}` in unquoted/double-quoted
 values using a private environment with checkout `PWD` and earlier dotenv
 assignments. Single-quoted values and escaped dollars stay literal. Parse the
diff --git a/scripts/support_bundle.py b/scripts/support_bundle.py
index 4aaac50bfe..fdb3461fb9 100644
--- a/scripts/support_bundle.py
+++ b/scripts/support_bundle.py
@@ -12,6 +12,7 @@ import subprocess
 import sys
 import zipfile
 from datetime import UTC, datetime
+from io import StringIO
 from pathlib import Path
 from typing import Any
 
@@ -283,14 +284,16 @@ def _thread_data_roots(project_root: Path) -> list[tuple[Path, str]]:
     if env_file.is_file():
         try:
             from dotenv.parser import parse_stream
-        except ImportError:
-            # Diagnostics must still work in an incomplete backend environment.
+
+            contents = env_file.read_text(encoding="utf-8-sig")
+        except (ImportError, OSError, UnicodeError):
+            # Diagnostics must still work with a broken environment or unreadable .env.
             pass
         else:
             # serve.sh changes to the checkout before sourcing .env. Keep its
             # assignment order in a private mapping; never export parsed secrets.
             environment = {**os.environ, "PWD": str(project_root.resolve())}
-            with env_file.open(encoding="utf-8-sig") as stream:
+            with StringIO(contents) as stream:
                 for binding in parse_stream(stream):
                     if not binding.key or binding.value is None or binding.error:
                         continue