diff --git a/scripts/apply-workflow-pins-remote.sh b/scripts/apply-workflow-pins-remote.sh
index b7594cae2..ae591975c 100755
--- a/scripts/apply-workflow-pins-remote.sh
+++ b/scripts/apply-workflow-pins-remote.sh
@@ -306,6 +306,10 @@ list_repos() {
 # The REMOTE content is the only evidence: a local checkout can be arbitrarily
 # stale, and reading one is what produced a false "285 callers track main"
 # census on 2026-09-15.
+# Returns non-zero when the answer is UNKNOWN (rate limit, 5xx, a file that
+# would not download). Only a 404 is "no workflows". Returning 0 on failure
+# made a rate-limited repo vanish from the census while `walked N` still
+# counted it (measured 2026-10-02, shared 5,000/h token exhausted mid-run).
 fetch_workflows() {
   local repo="$1" dest="$2" owner="${1%%/*}" name="${1##*/}" resp
   mkdir -p "$dest"
@@ -346,15 +350,17 @@ fetch_workflows() {
   # query cannot express. The REMOTE content is the only evidence either way —
   # reading a local checkout is what produced a false "285 callers track main"
   # census on 2026-09-15.
-  local fname
-  gh api "repos/${repo}/contents/.github/workflows" \
-     --jq '.[] | select(.type == "file") | .name' 2>/dev/null \
-  | grep -E '\.ya?ml$' \
-  | while IFS= read -r fname; do
-      gh api "repos/${repo}/contents/.github/workflows/${fname}" \
-         -H 'Accept: application/vnd.github.raw' > "${dest}/${fname}" 2>/dev/null \
-        || rm -f "${dest}/${fname}"
-    done
+  local fname listing
+  if ! listing=$(gh api "repos/${repo}/contents/.github/workflows" \
+                   --jq '.[] | select(.type == "file") | .name' 2>&1); then
+    case "$listing" in *"HTTP 404"*) return 0 ;; esac
+    return 1
+  fi
+  for fname in $(printf '%s\n' "$listing" | grep -E '\.ya?ml$'); do
+    gh api "repos/${repo}/contents/.github/workflows/${fname}" \
+       -H 'Accept: application/vnd.github.raw' > "${dest}/${fname}" 2>/dev/null \
+      || { rm -f "${dest}/${fname}"; return 1; }
+  done
   return 0
 }
 
@@ -449,13 +455,18 @@ main() {
   WORKDIR=$(mktemp -d); trap 'rm -rf "${WORKDIR:-}"' EXIT
   local repos n=0
   if [ -n "$ONLY_REPO" ]; then repos="$ONLY_REPO"; else repos=$(list_repos); fi
+  [ -n "$repos" ] || { log "FATAL: enumerated zero repositories for ${OWNERS} (rate limit or auth?). Refusing to report an empty census."; exit 1; }
 
   local repo
   for repo in $repos; do
     [ "$LIMIT" -gt 0 ] && [ "$n" -ge "$LIMIT" ] && break
     n=$((n+1))
     local rdir="${WORKDIR}/$(echo "$repo" | tr '/' '_')"
-    fetch_workflows "$repo" "$rdir"
+    if ! fetch_workflows "$repo" "$rdir"; then
+      log "  FETCH-FAILED ${repo}: workflows could not be read; NOT classified"
+      printf '%s\t-\tFETCH-FAILED\t-\n' "$repo" >> "$tsv"
+      continue
+    fi
     local found=0 changed=() wf base st detail
     shopt -s nullglob
     for wf in "$rdir"/*.yml "$rdir"/*.yaml; do
@@ -503,4 +514,6 @@ main() {
   rm -f "$tsv"
 }
 
-main "$@"
+if [ "${BASH_SOURCE[0]}" = "$0" ]; then
+  main "$@"
+fi
diff --git a/tests/test_apply_workflow_pins_remote.sh b/tests/test_apply_workflow_pins_remote.sh
index 5a1ffa168..2e3351fd8 100755
--- a/tests/test_apply_workflow_pins_remote.sh
+++ b/tests/test_apply_workflow_pins_remote.sh
@@ -134,6 +134,55 @@ kill_mutant illegal_repair_still_illegal \
   's@\@\$\{target\}@\@@g' \
   "FAIL illegal repair"
 
+# --- 3. fetch_workflows fails CLOSED -----------------------------------------
+# A rate-limited repo used to come back as "no workflows": fetch_workflows
+# returned 0 on every failure, so the census dropped the repo while `walked N`
+# still counted it (2026-10-02). Only a 404 may read as "nothing here".
+echo "== 3. fetch failures are reported, not swallowed =="
+STUB="$TMP/stub"; mkdir -p "$STUB"
+cat > "$STUB/gh" <<'EOF'
+#!/usr/bin/env bash
+case "$*" in
+  "api graphql"*) exit 1 ;;   # force the REST fallback
+  *contents/.github/workflows/*)
+    [ "${FILE_FAIL:-}" = 1 ] && { echo "gh: rate limit (HTTP 403)" >&2; exit 1; }
+    echo 'on: push'; exit 0 ;;
+  *contents/.github/workflows*)
+    case "${LIST:-200}" in
+      200) echo ci.yml; exit 0 ;;
+      404) echo "gh: Not Found (HTTP 404)" >&2; exit 1 ;;
+      *)   echo "gh: API rate limit exceeded (HTTP 403)" >&2; exit 1 ;;
+    esac ;;
+esac
+exit 1
+EOF
+chmod +x "$STUB/gh"
+# fetch_case <label> <want-rc> <env...> — run fetch_workflows against the stub.
+fetch_case() {
+  local label="$1" want="$2"; shift 2
+  local got
+  env PATH="$STUB:$PATH" "$@" bash -c 'source "$1"; fetch_workflows o/r "$2"' _ \
+      "${APPLIER_UNDER_TEST:-$APPLIER}" "$TMP/fetch.$label" >/dev/null 2>&1
+  got=$?
+  if [ "$got" = "$want" ]; then pass "fetch: $label (rc=$got)"; else fail "fetch: $label — expected rc=$want, got rc=$got"; fi
+}
+fetch_case "listing ok"            0 LIST=200
+fetch_case "no workflows dir (404)" 0 LIST=404
+fetch_case "rate-limited listing"   1 LIST=403
+fetch_case "file download fails"    1 LIST=200 FILE_FAIL=1
+[ -s "$TMP/fetch.listing ok/ci.yml" ] && pass "fetch: file content written" || fail "fetch: ci.yml not written"
+
+# Mutant: restore the old `return 0` on a failed listing. It must turn red.
+M="$TMP/mutant_fail_open.sh"; cp "$APPLIER" "$M"
+sed -i 's@^    return 1$@    return 0@' "$M"
+if cmp -s "$APPLIER" "$M" || ! bash -n "$M"; then
+  fail "fail-open mutant did not apply cleanly"
+else
+  out=$(APPLIER_UNDER_TEST="$M" fetch_case "MUTANT rate-limited listing" 1 LIST=403 2>&1)
+  case "$out" in *FAIL*) pass "mutant 'fetch_fail_open' killed by the rate-limit control" ;;
+                 *) fail "mutant 'fetch_fail_open' stayed GREEN" ;; esac
+fi
+
 echo
 if [ "$rc" -ne 0 ]; then echo "RESULT: FAILED" >&2; else echo "RESULT: all checks passed"; fi
 exit $rc