diff --git a/tests/tools/test_file_operations.py b/tests/tools/test_file_operations.py
index e80938d3ef7a6..7be49c51c31de 100644
--- a/tests/tools/test_file_operations.py
+++ b/tests/tools/test_file_operations.py
@@ -615,3 +615,61 @@ class TestAtomicWriteNewFilePermissions:
         assert result.error is None, f"write failed: {result.error}"
         assert dest.read_text() == "#!/bin/sh\necho updated\n"
         assert dest.stat().st_mode & 0o777 == 0o755
+
+
+class TestAtomicWriteThroughSymlink:
+    """_atomic_write must edit a symlink's target, not replace the link.
+
+    Regression: the temp-file + ``mv`` swap replaced the symlink itself with a
+    plain file, orphaning the real target and destroying the link (data-loss).
+    """
+
+    def test_write_follows_symlink_and_preserves_link(self, tmp_path):
+        ops = ShellFileOperations(make_real_subprocess_env(str(tmp_path)))
+        real = tmp_path / "real.txt"
+        link = tmp_path / "link.txt"
+        real.write_text("original\n")
+        link.symlink_to(real)
+
+        result = ops.write_file(str(link), "newcontent\n")
+
+        assert result.error is None, f"write failed: {result.error}"
+        # The link must survive as a symlink...
+        assert link.is_symlink(), "symlink was replaced by a plain file"
+        # ...and the real target must carry the new content.
+        assert real.read_text() == "newcontent\n"
+        assert os.path.realpath(link) == str(real)
+
+    def test_write_through_broken_symlink_falls_back(self, tmp_path):
+        """A broken link resolves through readlink -f and creates the target."""
+        ops = ShellFileOperations(make_real_subprocess_env(str(tmp_path)))
+        target = tmp_path / "target.txt"
+        link = tmp_path / "broken.lnk"
+        link.symlink_to(target)  # target does not exist yet
+
+        result = ops.write_file(str(link), "data\n")
+
+        assert result.error is None, f"write failed: {result.error}"
+        assert target.exists()
+        assert target.read_text() == "data\n"
+
+
+class TestReadNonUtf8IsBinary:
+    """Non-UTF-8 content must be flagged binary, not returned as lossy text.
+
+    Regression: the terminal env decodes stdout with errors="replace", turning
+    every non-UTF-8 byte into U+FFFD before _is_likely_binary sees it. U+FFFD is
+    "printable", so the non-printable ratio never caught it, and a
+    read→edit→write round-trip would overwrite the original bytes with mojibake.
+    """
+
+    def test_replacement_char_sample_flagged_binary(self, tmp_path):
+        ops = ShellFileOperations(make_real_subprocess_env(str(tmp_path)))
+        # A latin-1 file decoded with errors="replace" yields U+FFFD chars.
+        lossy_sample = "caf\ufffd r\ufffdsum\ufffd\n"
+        assert ops._is_likely_binary("notes.txt", lossy_sample) is True
+
+    def test_plain_utf8_text_not_flagged(self, tmp_path):
+        ops = ShellFileOperations(make_real_subprocess_env(str(tmp_path)))
+        # Proper UTF-8 (including non-ASCII) must still read as text.
+        assert ops._is_likely_binary("notes.txt", "café résumé\nsecond\n") is False
diff --git a/tools/file_operations.py b/tools/file_operations.py
index d0d1f53a833ee..59224325d885c 100644
--- a/tools/file_operations.py
+++ b/tools/file_operations.py
@@ -884,6 +884,17 @@ class ShellFileOperations(FileOperations):
         
         # Content analysis: >30% non-printable chars = binary
         if content_sample:
+            # Undecodable bytes: the terminal env decodes stdout with
+            # errors="replace", so any non-UTF-8 byte arrives here already
+            # turned into U+FFFD. That char is "printable" (ord 65533), so the
+            # non-printable ratio below never catches it — and returning the
+            # lossy text would let a read→edit→write round-trip silently
+            # overwrite the original bytes with mojibake. Treat a file whose
+            # sample carries the replacement char as binary (read-only) so the
+            # agent can't corrupt it. Legitimate UTF-8 text effectively never
+            # contains U+FFFD.
+            if "\ufffd" in content_sample[:1000]:
+                return True
             non_printable = sum(1 for c in content_sample[:1000]
                                if ord(c) < 32 and c not in '\n\r\t')
             return non_printable / min(len(content_sample), 1000) > 0.30
@@ -1022,11 +1033,21 @@ class ShellFileOperations(FileOperations):
         script = (
             "set -e; "
             f"d={q_parent}; t={q_path}; "
+            # Follow a symlink target so we edit the file the link points at,
+            # rather than replacing the symlink itself with a plain file (which
+            # orphans the real target and destroys the link). Recompute the
+            # temp dir from the RESOLVED target so `mv` stays same-filesystem
+            # atomic. Best-effort: a broken link or missing readlink/realpath
+            # falls back to the original path (pre-fix behavior, no regression).
+            'if [ -L "$t" ]; then '
+            'rt="$(readlink -f "$t" 2>/dev/null || realpath "$t" 2>/dev/null || true)"; '
+            '[ -n "$rt" ] && { t="$rt"; d="$(dirname "$t")"; }; '
+            "fi; "
             'tmp="$(mktemp -p "$d" ' + tmpl + ' 2>/dev/null '
             '|| mktemp "$d/.hermes-tmp.$$.XXXXXX" 2>/dev/null '
             '|| { tmp="$d/.hermes-tmp.$$"; : > "$tmp" && echo "$tmp"; })"; '
             '[ -n "$tmp" ] || { echo "atomic write: could not create temp file" >&2; exit 1; }; '
-            "trap 'rm -f \"$tmp\"' EXIT; "
+            "trap 'rm -f \\\"$tmp\\\"' EXIT; "
             # preserve mode of an existing target (best-effort, never fatal)
             'if [ -e "$t" ]; then '
             'm="$(stat -c%a "$t" 2>/dev/null || stat -f%Lp "$t" 2>/dev/null || true)"; '