diff --git a/.agents/scripts/supervisor/deploy.sh b/.agents/scripts/supervisor/deploy.sh
index 69550d7b14..09ff6d8027 100755
--- a/.agents/scripts/supervisor/deploy.sh
+++ b/.agents/scripts/supervisor/deploy.sh
@@ -2644,7 +2644,11 @@ run_verify_checks() {
 			;;
 		shellcheck)
 			if command -v shellcheck &>/dev/null; then
-				if shellcheck "$repo/$check_arg" 2>>"$SUPERVISOR_LOG"; then
+				# t1041: Use -S warning -x to match CI severity threshold.
+				# CI uses -S error; verify uses -S warning (catches warnings+errors
+				# but not info/style like SC2016/SC1091 which are pre-existing noise).
+				# -x follows source directives so sourced files don't cause SC1091.
+				if shellcheck -S warning -x "$repo/$check_arg" 2>>"$SUPERVISOR_LOG"; then
 					log_success "    PASS: shellcheck $check_arg"
 				else
 					log_error "    FAIL: shellcheck $check_arg"
diff --git a/.agents/scripts/supervisor/todo-sync.sh b/.agents/scripts/supervisor/todo-sync.sh
index 8ce6ccc80e..4575ed8503 100755
--- a/.agents/scripts/supervisor/todo-sync.sh
+++ b/.agents/scripts/supervisor/todo-sync.sh
@@ -1038,13 +1038,15 @@ cmd_reconcile_db_todo() {
 	fi
 
 	# --- Gap 2: TODO.md [x] but DB still in non-terminal state ---
-	# Terminal states: complete, deployed, verified, failed, blocked, cancelled
+	# Terminal states: complete, deployed, verified, failed, blocked, cancelled, verify_failed
 	# Non-terminal: queued, dispatched, running, evaluating, retrying,
-	#   pr_review, review_triage, merging, merged, deploying, verifying, verify_failed
+	#   pr_review, review_triage, merging, merged, deploying, verifying
+	# t1041: verify_failed is excluded — it's a meaningful state (PR merged+deployed
+	# but post-merge checks failed). Re-verification handles these, not reconciliation.
 	local all_db_tasks
 	all_db_tasks=$(db -separator '|' "$SUPERVISOR_DB" "
 		SELECT t.id, t.status FROM tasks t
-		WHERE t.status NOT IN ('complete', 'deployed', 'verified', 'failed', 'blocked', 'cancelled')
+		WHERE t.status NOT IN ('complete', 'deployed', 'verified', 'verify_failed', 'failed', 'blocked', 'cancelled')
 		$batch_filter
 		ORDER BY t.id;
 	")