diff --git a/hooks/SIMPLIFY-IGNORE.md b/hooks/SIMPLIFY-IGNORE.md
index 1db1e712..68ec06eb 100644
--- a/hooks/SIMPLIFY-IGNORE.md
+++ b/hooks/SIMPLIFY-IGNORE.md
@@ -54,7 +54,7 @@ One script, three hook events:
 |---|---|
 | `PreToolUse Read` | Backs up file, replaces blocks with `BLOCK_<hash>` placeholders in-place |
 | `PostToolUse Edit\|Write` | Expands placeholders back to real code, saves model's changes, re-filters |
-| `Stop` | Restores all files from backup when session ends |
+| `Stop` | Expands the placeholders left in each file on disk, so changes made outside `Edit`/`Write` survive; falls back to the backup only if no placeholder is left |
 
 Each block is content-hashed (8 hex chars via `shasum`/`sha1sum`) so the round-trip is unambiguous even if the model duplicates or reorders placeholders. Cache is project-scoped to prevent cross-session interference.
 
@@ -83,6 +83,7 @@ Backups are stored in `.claude/.simplify-ignore-cache/` within your project dire
 - **Single-line blocks hide the entire line.** If `simplify-ignore-start` and `simplify-ignore-end` appear on the same line as other code, the whole line is hidden from the model, not just the annotated portion. Use dedicated lines for annotations.
 - **Comment suffix detection covers `*/` and `-->` only.** Template engines with non-standard comment closers (ERB `%>`, Blade `--}}`) may produce unbalanced placeholders. Use `#` or `//` style comments instead.
 - **Fallback expansion is progressive, not exact.** If the model alters a placeholder's formatting (e.g. changes the reason text), the hook tries progressively simpler matches: full placeholder → prefix+hash+suffix → hash-only. The hash-only fallback may leave cosmetic debris (e.g. stray `:` or reason text). A warning is printed to stderr when this happens.
+- **A wholesale rewrite falls back to the backup.** If something replaces a filtered file's entire contents and removes every `BLOCK_<hash>` placeholder, the hook can no longer tell where the protected block belongs. At `Stop` it restores the backup and prints a warning, so that rewrite is lost. Changes that leave the placeholders in place — a `Bash` edit, a formatter, an external editor — are kept.
 - **File renaming leaves placeholders.** If the model renames or moves a file via a shell command, the new file will retain `BLOCK_<hash>` placeholders. The original code is saved as `<old-filename>.recovered` when the session stops. You must manually restore the recovered code into the new file.
 
 ## Requirements
diff --git a/hooks/simplify-ignore-test.sh b/hooks/simplify-ignore-test.sh
index 0d468e39..0a8ab065 100755
--- a/hooks/simplify-ignore-test.sh
+++ b/hooks/simplify-ignore-test.sh
@@ -247,6 +247,50 @@ else
   assert_eq "missing-jq guard surfaced" "1" "$(printf '%s' "$warning_out" | grep -c 'error: missing jq')"
 fi
 
+# ── Test 11: Stop keeps a change made outside Edit|Write ─────────────────
+printf '\nTest 11: Stop keeps a Bash write made after the last Edit\n'
+
+if ! command -v jq >/dev/null 2>&1; then
+  printf '  SKIP: full lifecycle needs jq (the hook exits at its jq guard)\n'
+else
+  PROJ="$TMPDIR/proj"
+  rm -rf "$PROJ"
+  mkdir -p "$PROJ/.claude"
+  TARGET="$PROJ/app.js"
+  cat > "$TARGET" <<'EOF'
+const editable = 1;
+/* simplify-ignore-start: perf-critical */
+const protectedValue = 42;
+/* simplify-ignore-end */
+EOF
+
+  hook_event() { printf '%s' "$1" | CLAUDE_PROJECT_DIR="$PROJ" bash hooks/simplify-ignore.sh; }
+  read_event=$(printf '{"tool_name":"Read","tool_input":{"file_path":"%s"}}' "$TARGET")
+  edit_event=$(printf '{"tool_name":"Edit","tool_input":{"file_path":"%s"}}' "$TARGET")
+
+  # PreToolUse Read → block hidden behind a placeholder, backup taken
+  hook_event "$read_event"
+  assert_eq "protected block hidden after Read" "1" "$(grep -c 'BLOCK_' "$TARGET")"
+  assert_eq "protected content off disk after Read" "0" "$(grep -c 'protectedValue' "$TARGET")"
+
+  # Model edits the filtered file → PostToolUse Edit refreshes the backup
+  printf 'const added = 3;\n' >> "$TARGET"
+  hook_event "$edit_event"
+
+  # A later write through Bash — no Edit or Write event follows it
+  sed 's/const editable = 1;/const editable = 2;/' "$TARGET" > "$TMPDIR/bash-write.js"
+  cat "$TMPDIR/bash-write.js" > "$TARGET"
+
+  # Stop
+  hook_event '{}'
+
+  assert_eq "Bash write survives Stop" "1" "$(grep -c 'const editable = 2;' "$TARGET")"
+  assert_eq "stale backup value not restored" "0" "$(grep -c 'const editable = 1;' "$TARGET")"
+  assert_eq "edit made through Edit survives Stop" "1" "$(grep -c 'const added = 3;' "$TARGET")"
+  assert_eq "protected block back on disk" "1" "$(grep -c 'const protectedValue = 42;' "$TARGET")"
+  assert_eq "no placeholder left after Stop" "0" "$(grep -c 'BLOCK_' "$TARGET")"
+fi
+
 # ── Summary ──────────────────────────────────────────────────────────────
 printf '\n══════════════════════════════════════════\n'
 printf 'Results: %d passed, %d failed\n' "$PASS" "$FAIL"
diff --git a/hooks/simplify-ignore.sh b/hooks/simplify-ignore.sh
index a93c467c..58b3d90a 100755
--- a/hooks/simplify-ignore.sh
+++ b/hooks/simplify-ignore.sh
@@ -4,10 +4,13 @@
 # PreToolUse Read   → backs up file, replaces blocks with BLOCK_<hash> in-place
 # PostToolUse Edit  → expands placeholders, re-filters so file stays hidden
 # PostToolUse Write → expands placeholders, re-filters so file stays hidden
-# Stop              → restores real file content from backup
+# Stop              → expands the placeholders still in the file on disk, so a
+#                     change made by any route survives; the backup is used
+#                     only when no placeholder is left to expand
 #
 # The file on disk ALWAYS has placeholders while the session is active.
-# The real content (with model's changes applied) lives in the backup.
+# The real content is that file with its placeholders expanded; the backup
+# holds the last state the hook itself saw.
 #
 # Dependencies: jq, shasum or sha1sum (auto-detected)
 
@@ -141,7 +144,87 @@ ${line}"
   [ $count -gt 0 ] && return 0 || return 1
 }
 
-# ── Stop: restore all files from backup ───────────────────────────────────────
+# ── expand_file: replace BLOCK_<hash> placeholders with the real block code ───
+# Reads $1 (source), writes the expanded version to $2 (dest), using the blocks
+# cached under $3 (file id). Warns on placeholders that were altered or deleted.
+expand_file() {
+  local src="$1" dest="$2" fid="$3"
+  local line bf h bp bs br placeholder block_content esc_placeholder esc_fuzzy bh first_line
+  rm -f "$dest"
+  while IFS= read -r line || [ -n "$line" ]; do
+    case "$line" in *BLOCK_*)
+      # Expand all placeholders on this line (supports multiple per line)
+      for bf in "$CACHE/${fid}".block.*; do
+        [ -f "$bf" ] || continue
+        h="${bf##*.}"
+        case "$line" in *"BLOCK_${h}"*)
+          # Reconstruct the exact placeholder pattern
+          bp=""; bs=""; br=""
+          [ -f "$CACHE/${fid}.prefix.${h}" ] && bp=$(cat "$CACHE/${fid}.prefix.${h}")
+          [ -f "$CACHE/${fid}.suffix.${h}" ] && bs=$(cat "$CACHE/${fid}.suffix.${h}")
+          [ -f "$CACHE/${fid}.reason.${h}" ] && br=$(cat "$CACHE/${fid}.reason.${h}")
+          if [ -n "$br" ]; then
+            placeholder="${bp}BLOCK_${h}: ${br}${bs}"
+          else
+            placeholder="${bp}BLOCK_${h}${bs}"
+          fi
+          block_content=$(cat "$bf"; printf x); block_content="${block_content%x}"
+          # Escape glob metacharacters (* ? [ \) in the pattern
+          esc_placeholder=$(escape_glob "$placeholder")
+          # Bash native substitution (// = global replace): replace placeholder, keep surrounding code
+          line="${line//$esc_placeholder/$block_content}"
+          # Fallback: if model altered the reason text, try without reason
+          # (only trigger if BLOCK_hash is still present AND wasn't in the original block content)
+          case "$block_content" in *"BLOCK_${h}"*) ;; *)
+            case "$line" in *"BLOCK_${h}"*)
+              printf 'Warning: placeholder BLOCK_%s was modified by model, using fuzzy match\n' "$h" >&2
+              esc_fuzzy=$(escape_glob "${bp}BLOCK_${h}${bs}")
+              line="${line//$esc_fuzzy/$block_content}"
+              # Last resort: match just the hash token
+              case "$line" in *"BLOCK_${h}"*)
+                line="${line//BLOCK_${h}/$block_content}"
+              ;; esac
+            ;; esac
+          ;; esac
+        ;; esac
+      done
+    ;; esac
+    printf '%s\n' "$line" >> "$dest"
+  done < "$src"
+  # Preserve trailing newline status
+  if [ -s "$dest" ] && [ -s "$src" ] && [ -n "$(tail -c 1 "$src")" ]; then
+    perl -pe 'chomp if eof' "$dest" > "${dest}.nnl" && \
+      cat "${dest}.nnl" > "$dest" && rm -f "${dest}.nnl"
+  fi
+  # Warn if model deleted a protected block entirely
+  for bf in "$CACHE/${fid}".block.*; do
+    [ -f "$bf" ] || continue
+    bh="${bf##*.}"
+    # After expansion, blocks appear as original code (simplify-ignore-start).
+    # If neither the expanded code nor the placeholder is in EXPANDED, it was deleted.
+    if ! grep -qF "BLOCK_${bh}" "$dest" 2>/dev/null; then
+      # Get first line of block to check if it was expanded back
+      first_line=$(head -1 "$bf")
+      if ! grep -qF "$first_line" "$dest" 2>/dev/null; then
+        printf 'Warning: protected block BLOCK_%s was deleted by model\n' "$bh" >&2
+      fi
+    fi
+  done
+  return 0
+}
+
+# ── has_placeholders: is a cached BLOCK_<hash> for $2 still present in file $1? ─
+has_placeholders() {
+  local f="$1" fid="$2" bf h
+  for bf in "$CACHE/${fid}".block.*; do
+    [ -f "$bf" ] || continue
+    h="${bf##*.}"
+    grep -qF "BLOCK_${h}" "$f" 2>/dev/null && return 0
+  done
+  return 1
+}
+
+# ── Stop: expand each cached file in place, backup only as fallback ──────────
 if [ -z "$TOOL_NAME" ]; then
   [ -d "$CACHE" ] || exit 0
   for bak in "$CACHE"/*.bak; do
@@ -151,7 +234,20 @@ if [ -z "$TOOL_NAME" ]; then
     [ -f "$pathfile" ] || { rm -f "$bak"; continue; }
     orig=$(cat "$pathfile")
     if [ -f "$orig" ]; then
-      cat "$bak" > "$orig"
+      # A change can reach the file through a route that fires no Edit or Write
+      # event (a Bash command, a formatter, an external editor), and the backup
+      # is stale for all of them. Expand what is on disk rather than overwrite it.
+      if has_placeholders "$orig" "$fid"; then
+        EXPANDED="$CACHE/${fid}.$$.expanded"
+        expand_file "$orig" "$EXPANDED" "$fid"
+        cat "$EXPANDED" > "$orig"
+        rm -f "$EXPANDED"
+      else
+        # Nothing left to expand — the file was rewritten wholesale, so the
+        # backup is the only remaining copy of the protected blocks.
+        printf 'Warning: no BLOCK_ placeholder left in %s, restored from backup\n' "$orig" >&2
+        cat "$bak" > "$orig"
+      fi
       rm -f "$bak" "$pathfile" "$CACHE/${fid}".block.* "$CACHE/${fid}".reason.* "$CACHE/${fid}".prefix.* "$CACHE/${fid}".suffix.*
       rmdir "$CACHE/${fid}.lock" 2>/dev/null
     else
@@ -223,66 +319,7 @@ if [ "$TOOL_NAME" = "Edit" ] || [ "$TOOL_NAME" = "Write" ]; then
 
   # Expand placeholders, preserving any inline code the model added around them
   EXPANDED="$CACHE/${ID}.$$.expanded"
-  rm -f "$EXPANDED"
-  while IFS= read -r line || [ -n "$line" ]; do
-    case "$line" in *BLOCK_*)
-      # Expand all placeholders on this line (supports multiple per line)
-      for bf in "$CACHE/${ID}".block.*; do
-        [ -f "$bf" ] || continue
-        h="${bf##*.}"
-        case "$line" in *"BLOCK_${h}"*)
-          # Reconstruct the exact placeholder pattern
-          bp=""; bs=""; br=""
-          [ -f "$CACHE/${ID}.prefix.${h}" ] && bp=$(cat "$CACHE/${ID}.prefix.${h}")
-          [ -f "$CACHE/${ID}.suffix.${h}" ] && bs=$(cat "$CACHE/${ID}.suffix.${h}")
-          [ -f "$CACHE/${ID}.reason.${h}" ] && br=$(cat "$CACHE/${ID}.reason.${h}")
-          if [ -n "$br" ]; then
-            placeholder="${bp}BLOCK_${h}: ${br}${bs}"
-          else
-            placeholder="${bp}BLOCK_${h}${bs}"
-          fi
-          block_content=$(cat "$bf"; printf x); block_content="${block_content%x}"
-          # Escape glob metacharacters (* ? [ \) in the pattern
-          esc_placeholder=$(escape_glob "$placeholder")
-          # Bash native substitution (// = global replace): replace placeholder, keep surrounding code
-          line="${line//$esc_placeholder/$block_content}"
-          # Fallback: if model altered the reason text, try without reason
-          # (only trigger if BLOCK_hash is still present AND wasn't in the original block content)
-          case "$block_content" in *"BLOCK_${h}"*) ;; *)
-            case "$line" in *"BLOCK_${h}"*)
-              printf 'Warning: placeholder BLOCK_%s was modified by model, using fuzzy match\n' "$h" >&2
-              esc_fuzzy=$(escape_glob "${bp}BLOCK_${h}${bs}")
-              line="${line//$esc_fuzzy/$block_content}"
-              # Last resort: match just the hash token
-              case "$line" in *"BLOCK_${h}"*)
-                line="${line//BLOCK_${h}/$block_content}"
-              ;; esac
-            ;; esac
-          ;; esac
-        ;; esac
-      done
-    ;; esac
-    printf '%s\n' "$line" >> "$EXPANDED"
-  done < "$FILE_PATH"
-  # Preserve trailing newline status
-  if [ -s "$EXPANDED" ] && [ -s "$FILE_PATH" ] && [ -n "$(tail -c 1 "$FILE_PATH")" ]; then
-    perl -pe 'chomp if eof' "$EXPANDED" > "${EXPANDED}.nnl" && \
-      cat "${EXPANDED}.nnl" > "$EXPANDED" && rm -f "${EXPANDED}.nnl"
-  fi
-  # Warn if model deleted a protected block entirely
-  for bf in "$CACHE/${ID}".block.*; do
-    [ -f "$bf" ] || continue
-    bh="${bf##*.}"
-    # After expansion, blocks appear as original code (simplify-ignore-start).
-    # If neither the expanded code nor the placeholder is in EXPANDED, it was deleted.
-    if ! grep -qF "BLOCK_${bh}" "$EXPANDED" 2>/dev/null; then
-      # Get first line of block to check if it was expanded back
-      first_line=$(head -1 "$bf")
-      if ! grep -qF "$first_line" "$EXPANDED" 2>/dev/null; then
-        printf 'Warning: protected block BLOCK_%s was deleted by model\n' "$bh" >&2
-      fi
-    fi
-  done
+  expand_file "$FILE_PATH" "$EXPANDED" "$ID"
   # Preserve inode and permissions
   cat "$EXPANDED" > "$FILE_PATH"
   rm -f "$EXPANDED"