diff --git a/docs/EVALUATION_PLAN.md b/docs/EVALUATION_PLAN.md
index 39d72848f..25a8f6aaf 100644
--- a/docs/EVALUATION_PLAN.md
+++ b/docs/EVALUATION_PLAN.md
@@ -299,9 +299,13 @@ for lang in $ALL_LANGS; do                      # ALL_LANGS = full 159-name list
 
   # --- step 8: delete THIS language's index so the next is cold, then mark done ---
   # The graph session (steps 4-7) may still have a daemon running under the kept
-  # CBM_RUNTIME_DIR (exported above); stop it before its root goes away.
-  ~/.local/bin/codebase-memory-mcp daemon stop || true
-  rm -rf -- "$CBM_BENCH_RUNTIME_ROOT"
+  # CBM_RUNTIME_DIR (exported above); stop it before its root goes away. A refused
+  # stop (a session still attached) means the root is still in use: keep it.
+  if ~/.local/bin/codebase-memory-mcp daemon stop; then
+    rm -rf -- "$CBM_BENCH_RUNTIME_ROOT"
+  else
+    echo "$lang: daemon under $CBM_RUNTIME_DIR did not stop; keeping $CBM_BENCH_RUNTIME_ROOT" >&2
+  fi
   manifest_mark_done "$lang" "$index_ms"
 done
 ```
diff --git a/scripts/benchmark-index.sh b/scripts/benchmark-index.sh
index a8db36828..792ec9feb 100755
--- a/scripts/benchmark-index.sh
+++ b/scripts/benchmark-index.sh
@@ -33,11 +33,21 @@ cbm_test_runtime_init
 # including its removal — passes to the caller. A failed run cleans up
 # regardless: there is no index worth keeping, and nothing must leak. Never on
 # by default, or an unattended run accumulates one root per language.
+#
+# The handoff promises a stopped daemon, so it is written only once
+# `daemon stop` succeeded. A refused stop (a client still committed to the
+# daemon, or no answer) fails the run with the product's explanation, writes
+# no handoff, and keeps the root without cleaning it up: the daemon may still
+# be using it, and the operator decides what happens to it.
 bench_finish() {
-  local rc=$?
+  local rc=$? stop_out=""
   [ -z "${BENCH_TMP:-}" ] || rm -rf -- "$BENCH_TMP" || true
   if [ "$rc" -eq 0 ] && [ -n "${CBM_BENCH_KEEP_RUNTIME:-}" ] && [ -d "${OUT:-}" ]; then
-    "$BINARY" daemon stop >/dev/null 2>&1 || true
+    if ! stop_out=$("$BINARY" daemon stop 2>&1); then
+      echo "  $LANG: private daemon did not stop; runtime kept at $CBM_TEST_RUNTIME_ROOT, no handoff written" >&2
+      [ -z "$stop_out" ] || printf '%s\n' "$stop_out" >&2
+      exit 1
+    fi
     printf 'CBM_BENCH_RUNTIME_ROOT=%q\nCBM_RUNTIME_DIR=%q\nCBM_CACHE_DIR=%q\n' \
       "$CBM_TEST_RUNTIME_ROOT" "$CBM_RUNTIME_DIR" "$CBM_CACHE_DIR" > "$OUT/runtime-root.txt"
     echo "  $LANG: runtime kept at $CBM_TEST_RUNTIME_ROOT; paths in $OUT/runtime-root.txt" >&2