diff --git a/.claude/scripts/loop-census.sh b/.claude/scripts/loop-census.sh
index 7006039..8bdcc70 100644
--- a/.claude/scripts/loop-census.sh
+++ b/.claude/scripts/loop-census.sh
@@ -29,6 +29,12 @@
 #                               hasn't reached PR stage. A tick uses this to
 #                               avoid double-spawning an orchestrator for an
 #                               issue that already has a worktree in progress.
+#                               A REMOTE-ONLY branch match (no local branch of
+#                               the same name) that turns out to be a stale
+#                               ref for an issue whose PR already MERGED is
+#                               ignored (branch=none) instead of counting as
+#                               in_flight forever — see STALE-MERGED-REMOTE
+#                               below (issue #158).
 #   stalled=<n> age_min=<m>      one line PER in_flight issue whose most recent
 #                               events.jsonl activity is older than the stall
 #                               threshold (issue #98) — see STALL DETECTION
@@ -117,6 +123,26 @@
 # one candidate was otherwise eligible; with zero eligible candidates,
 # advance_ready stays "none" exactly as before this feature.
 #
+# --- STALE-MERGED-REMOTE (issue #158) ---------------------------------------
+# `git branch -a --list "*feat/issue-N-*"` matches BOTH local branches and
+# remote-tracking refs (`remotes/origin/...`). After a PR merges — even with
+# `gh pr merge --delete-branch` — the MAIN checkout's local remote-tracking
+# ref for that branch can survive until pruned (`git fetch --prune` /
+# `git remote prune`). Without this guard, a still-open issue whose partial
+# PR already merged would keep matching that stale ref FOREVER, so census
+# would report it in_flight forever — wedging advance_ready and eventually
+# tripping stall/escalation for an issue that in truth has no active branch.
+#
+# Fix: when the ONLY match for an issue is a remote-tracking ref (no local
+# branch of the same name), look up whether a MERGED PR exists for that bare
+# branch name. If one does, treat the issue as branch=none (ignore the stale
+# ref) — it neither counts as in_flight nor blocks advance_ready. If no
+# merged PR is found (the common case: work genuinely in progress, only
+# pushed, local branch since deleted), remote-only in_flight is preserved
+# exactly as before this fix. A genuine LOCAL branch match is unaffected —
+# it always wins over a remote-only one, so this only changes behavior for
+# the specific remote-only-and-already-merged case.
+#
 # --- STALL DETECTION (issue #98) --------------------------------------------
 # An `in_flight` issue (feat/issue-N-* branch exists, no open PR yet) can sit
 # forever if the driver that created it hung or died without ever reaching
@@ -348,12 +374,51 @@ while IFS=$'\t' read -r num labels title; do
   done <<< "$module_labels"
   [ "$hit" -eq 1 ] || continue
   planned_count=$((planned_count + 1))
-  # Existing feat/issue-<n>-* branch (local or remote) means it's already in flight.
-  # NOTE: `| head -1` can make `git` see SIGPIPE (exit 141) if head closes the
-  # pipe before git finishes writing; under `set -euo pipefail` that would abort
-  # this whole script. `|| true` on the assignment absorbs that non-fatal
-  # pipeline failure — the captured output (head's one line) is unaffected.
-  branch=$(git -C "$root" branch -a --list "*feat/issue-$num-*" | head -1 | sed 's/^[* ]*//;s|^remotes/||') || true
+  # Existing feat/issue-<n>-* branch: a LOCAL branch means genuinely in_flight
+  # (branch #158) regardless of GitHub state. A REMOTE-ONLY match
+  # (`remotes/origin/...`, no local branch of the same name) is only treated
+  # as "existing" if it is NOT a stale ref left over from an already-merged
+  # PR (issue #158): `git branch -a --list` matches BOTH local branches and
+  # remote-tracking refs, and after a PR merges (even with
+  # `gh pr merge --delete-branch`) the MAIN checkout's local remote-tracking
+  # ref for it can survive until pruned — so a still-open issue whose partial
+  # PR already merged would otherwise match that stale ref FOREVER and never
+  # advance (wedges advance_ready, triggers false stall/escalation). A local
+  # match, when present, always wins over a remote-only one.
+  local_branch=""
+  remote_branch=""
+  branch_lines=$(git -C "$root" branch -a --list "*feat/issue-$num-*" | sed 's/^[* ]*//') || true
+  if [ -n "$branch_lines" ]; then
+    while IFS= read -r bl; do
+      [ -z "$bl" ] && continue
+      case "$bl" in
+        remotes/*) [ -z "$remote_branch" ] && remote_branch="$bl" ;;
+        *) [ -z "$local_branch" ] && local_branch="$bl" ;;
+      esac
+    done <<< "$branch_lines"
+  fi
+
+  if [ -n "$local_branch" ]; then
+    branch="$local_branch"
+  elif [ -n "$remote_branch" ]; then
+    # Bare branch name (strip the "remotes/<remote>/" prefix, e.g.
+    # "remotes/origin/feat/issue-158-x" -> "feat/issue-158-x") to query gh
+    # for a merged PR under it. Only done on this remote-only path — never on
+    # the common local-branch path above — to avoid the extra gh call there.
+    # Guarded with `|| true` (transient gh failure degrades gracefully to "no
+    # merged PR found", i.e. the prior remote-only-stays-in_flight behavior;
+    # it must never abort the census under `set -euo pipefail`).
+    bare_branch="${remote_branch#remotes/*/}"
+    merged_count=$(gh pr list -R "$repo" --state merged --head "$bare_branch" --json number --jq 'length' 2>/dev/null) || true
+    case "$merged_count" in ''|*[!0-9]*) merged_count=0 ;; esac
+    if [ "$merged_count" -ge 1 ]; then
+      branch="none"  # stale remote-tracking ref for an already-merged PR — ignore it (issue #158)
+    else
+      branch="${remote_branch#remotes/}"
+    fi
+  else
+    branch="none"
+  fi
   [ -n "$branch" ] || branch="none"
   detail+="issue=$num branch=$branch title=$title"$'\n'
 
diff --git a/.claude/scripts/loop-census.test.sh b/.claude/scripts/loop-census.test.sh
index c973900..67d32a2 100644
--- a/.claude/scripts/loop-census.test.sh
+++ b/.claude/scripts/loop-census.test.sh
@@ -85,6 +85,11 @@ check() {
 #   - issue 100: a LOCAL branch feat/issue-100-w, which ALREADY has an open
 #                PR under its bare (exact, no prefix) name -> must NOT be
 #                in_flight (the plain exact-match control case).
+#   - issue 44:  a REMOTE-tracking-only branch feat/issue-44-m (pushed, local
+#                copy deleted, same shape as issue 42), but a MERGED PR
+#                already exists for it -> stale-merged-remote (issue #158):
+#                must report branch=none and NOT be in_flight, even though
+#                the remote-tracking ref itself still exists.
 # ---------------------------------------------------------------------------
 fixture="$work/fixture1"
 scripts_dir="$fixture/.claude/scripts"
@@ -122,18 +127,28 @@ EOF
 
 # Fake bot-gh.sh: no network, no real `gh` — dispatches on the subcommand and
 # a `--json` marker to canned, fixture-appropriate output.
+#   - `pr list --state merged --head <branch> ...`: merged-PR count for a
+#     bare branch name (issue #158) — 1 for feat/issue-44-m (the
+#     stale-merged-remote case), 0 for everything else (default). Checked
+#     BEFORE the headRefName/default branches below since it shares the `pr`
+#     subcommand but never carries the `headRefName` marker.
 #   - `pr list ... --json headRefName ...`: bare branch names of open PRs —
-#     issues 43 and 100 already have one; issue 42 does not (issue 4 has no
-#     branch, so it can't have a PR either).
+#     issues 43 and 100 already have one; issue 42 and 44 do not (issue 4 has
+#     no branch, so it can't have a PR either).
 #   - `pr list ... --json number ...`:       open PR count (2, matching above).
 #   - `issue list ...`:                      TSV `num<TAB>labels<TAB>title`
-#     for the four planned+module:test issues.
+#     for the five planned+module:test issues.
 cat > "$scripts_dir/bot-gh.sh" <<'EOF'
 #!/usr/bin/env bash
 case "$1" in
   repo) echo "acme/repo" ;;
   pr)
-    if printf '%s\n' "$*" | grep -q 'headRefName'; then
+    if printf '%s\n' "$*" | grep -q -- '--state merged'; then
+      case "$*" in
+        *"--head feat/issue-44-m"*) echo 1 ;;
+        *) echo 0 ;;
+      esac
+    elif printf '%s\n' "$*" | grep -q 'headRefName'; then
       printf '%s\n' "feat/issue-43-z"
       printf '%s\n' "feat/issue-100-w"
     else
@@ -144,6 +159,7 @@ case "$1" in
     printf '4\tplanned,module:test\tIssue four\n'
     printf '42\tplanned,module:test\tIssue forty two\n'
     printf '43\tplanned,module:test\tIssue forty three\n'
+    printf '44\tplanned,module:test\tIssue forty four\n'
     printf '100\tplanned,module:test\tIssue one hundred\n'
     ;;
   *) echo "fake-bot-gh.sh: unhandled args: $*" >&2; exit 1 ;;
@@ -193,6 +209,14 @@ git -C "$fixture" branch feat/issue-43-z main >/dev/null
 git -C "$fixture" push -q origin feat/issue-43-z >/dev/null 2>&1
 git -C "$fixture" branch -D feat/issue-43-z >/dev/null
 
+# issue 44: same shape as 42/43 (remote-tracking-only ref, local copy
+# deleted), but the fake bot-gh.sh reports a MERGED PR already exists for its
+# bare branch name — the stale-merged-remote case (issue #158): this ref must
+# be ignored (branch=none), not counted as in_flight forever.
+git -C "$fixture" branch feat/issue-44-m main >/dev/null
+git -C "$fixture" push -q origin feat/issue-44-m >/dev/null 2>&1
+git -C "$fixture" branch -D feat/issue-44-m >/dev/null
+
 # issue 100: LOCAL-only branch (never pushed) — exact-match control.
 git -C "$fixture" branch feat/issue-100-w main >/dev/null
 
@@ -208,8 +232,10 @@ check "issue 4 is NOT in_flight (no branch to be in flight with)" bash -c '! pri
 check "issue 42 (remote-only branch, no open PR) IS in_flight" bash -c 'printf "%s\n" "$1" | grep -qx "in_flight=42"' _ "$out"
 check "issue 43 (remote-only branch, already has an open PR via origin/ strip+suffix match) is NOT in_flight" bash -c '! printf "%s\n" "$1" | grep -qx "in_flight=43"' _ "$out"
 check "issue 100 (local branch, already has an open PR, exact-match control) is NOT in_flight" bash -c '! printf "%s\n" "$1" | grep -qx "in_flight=100"' _ "$out"
+check "issue 44 (remote-only branch, MERGED PR already exists) reports branch=none (issue #158)" bash -c 'printf "%s\n" "$1" | grep -q "^issue=44 branch=none"' _ "$out"
+check "issue 44 (stale merged remote-only ref) is NOT in_flight (issue #158)" bash -c '! printf "%s\n" "$1" | grep -qx "in_flight=44"' _ "$out"
 check "exactly one in_flight line total (only issue 42 qualifies)" bash -c '[ "$(printf "%s\n" "$1" | grep -c "^in_flight=")" -eq 1 ]' _ "$out"
-check "planned_issues=4 counted" bash -c 'printf "%s\n" "$1" | grep -qx "planned_issues=4"' _ "$out"
+check "planned_issues=5 counted" bash -c 'printf "%s\n" "$1" | grep -qx "planned_issues=5"' _ "$out"
 check "issue=42 branch line shows the origin-prefixed remote-tracking name" bash -c 'printf "%s\n" "$1" | grep -q "^issue=42 branch=origin/feat/issue-42-y"' _ "$out"
 check "ci_fix_prs=0 counted (no-op pr-ci-fix.sh stub, issue #96)" bash -c 'printf "%s\n" "$1" | grep -qx "ci_fix_prs=0"' _ "$out"
 check "comment_fix_prs=0 counted (no-op pr-comment-fix.sh stub, issue #96 part 2)" bash -c 'printf "%s\n" "$1" | grep -qx "comment_fix_prs=0"' _ "$out"