diff --git a/cmd/bd/ready.go b/cmd/bd/ready.go
index c94ef5a1..031f978e 100644
--- a/cmd/bd/ready.go
+++ b/cmd/bd/ready.go
@@ -269,6 +269,9 @@ var statsCmd = &cobra.Command{
 			fmt.Printf("Closed:            %d\n", stats.ClosedIssues)
 			fmt.Printf("Blocked:           %d\n", stats.BlockedIssues)
 			fmt.Printf("Ready:             %s\n", green(fmt.Sprintf("%d", stats.ReadyIssues)))
+			if stats.TombstoneIssues > 0 {
+				fmt.Printf("Deleted:           %d (tombstones)\n", stats.TombstoneIssues)
+			}
 			if stats.AverageLeadTime > 0 {
 				fmt.Printf("Avg Lead Time:     %.1f hours\n", stats.AverageLeadTime)
 			}
@@ -307,6 +310,9 @@ var statsCmd = &cobra.Command{
 		fmt.Printf("Closed:                 %d\n", stats.ClosedIssues)
 		fmt.Printf("Blocked:                %d\n", stats.BlockedIssues)
 		fmt.Printf("Ready:                  %s\n", green(fmt.Sprintf("%d", stats.ReadyIssues)))
+		if stats.TombstoneIssues > 0 {
+			fmt.Printf("Deleted:                %d (tombstones)\n", stats.TombstoneIssues)
+		}
 		if stats.EpicsEligibleForClosure > 0 {
 			fmt.Printf("Epics Ready to Close:   %s\n", green(fmt.Sprintf("%d", stats.EpicsEligibleForClosure)))
 		}
diff --git a/internal/storage/sqlite/events.go b/internal/storage/sqlite/events.go
index 9409102c..b34e301f 100644
--- a/internal/storage/sqlite/events.go
+++ b/internal/storage/sqlite/events.go
@@ -110,15 +110,16 @@ func (s *SQLiteStorage) GetEvents(ctx context.Context, issueID string, limit int
 func (s *SQLiteStorage) GetStatistics(ctx context.Context) (*types.Statistics, error) {
 	var stats types.Statistics
 
-	// Get counts
+	// Get counts (bd-nyt: exclude tombstones from TotalIssues, report separately)
 	err := s.db.QueryRowContext(ctx, `
 		SELECT
-			COUNT(*) as total,
+			COALESCE(SUM(CASE WHEN status != 'tombstone' THEN 1 ELSE 0 END), 0) as total,
 			COALESCE(SUM(CASE WHEN status = 'open' THEN 1 ELSE 0 END), 0) as open,
 			COALESCE(SUM(CASE WHEN status = 'in_progress' THEN 1 ELSE 0 END), 0) as in_progress,
-			COALESCE(SUM(CASE WHEN status = 'closed' THEN 1 ELSE 0 END), 0) as closed
+			COALESCE(SUM(CASE WHEN status = 'closed' THEN 1 ELSE 0 END), 0) as closed,
+			COALESCE(SUM(CASE WHEN status = 'tombstone' THEN 1 ELSE 0 END), 0) as tombstone
 		FROM issues
-	`).Scan(&stats.TotalIssues, &stats.OpenIssues, &stats.InProgressIssues, &stats.ClosedIssues)
+	`).Scan(&stats.TotalIssues, &stats.OpenIssues, &stats.InProgressIssues, &stats.ClosedIssues, &stats.TombstoneIssues)
 	if err != nil {
 		return nil, fmt.Errorf("failed to get issue counts: %w", err)
 	}
diff --git a/internal/storage/sqlite/migrations/018_tombstone_columns.go b/internal/storage/sqlite/migrations/018_tombstone_columns.go
index 6462fe17..32711f75 100644
--- a/internal/storage/sqlite/migrations/018_tombstone_columns.go
+++ b/internal/storage/sqlite/migrations/018_tombstone_columns.go
@@ -43,5 +43,12 @@ func MigrateTombstoneColumns(db *sql.DB) error {
 		}
 	}
 
+	// Add partial index on deleted_at for efficient TTL queries (bd-saa)
+	// Only indexes non-NULL values, making it very efficient for tombstone filtering
+	_, err := db.Exec(`CREATE INDEX IF NOT EXISTS idx_issues_deleted_at ON issues(deleted_at) WHERE deleted_at IS NOT NULL`)
+	if err != nil {
+		return fmt.Errorf("failed to create deleted_at index: %w", err)
+	}
+
 	return nil
 }
diff --git a/internal/storage/sqlite/queries.go b/internal/storage/sqlite/queries.go
index ee2fc01d..76ad6932 100644
--- a/internal/storage/sqlite/queries.go
+++ b/internal/storage/sqlite/queries.go
@@ -1186,6 +1186,10 @@ func (s *SQLiteStorage) SearchIssues(ctx context.Context, query string, filter t
 	if filter.Status != nil {
 		whereClauses = append(whereClauses, "status = ?")
 		args = append(args, *filter.Status)
+	} else if !filter.IncludeTombstones {
+		// Exclude tombstones by default unless explicitly filtering for them (bd-1bu)
+		whereClauses = append(whereClauses, "status != ?")
+		args = append(args, types.StatusTombstone)
 	}
 
 	if filter.Priority != nil {
diff --git a/internal/storage/sqlite/transaction.go b/internal/storage/sqlite/transaction.go
index d002808c..9689ee8b 100644
--- a/internal/storage/sqlite/transaction.go
+++ b/internal/storage/sqlite/transaction.go
@@ -919,6 +919,10 @@ func (t *sqliteTxStorage) SearchIssues(ctx context.Context, query string, filter
 	if filter.Status != nil {
 		whereClauses = append(whereClauses, "status = ?")
 		args = append(args, *filter.Status)
+	} else if !filter.IncludeTombstones {
+		// Exclude tombstones by default unless explicitly filtering for them (bd-1bu)
+		whereClauses = append(whereClauses, "status != ?")
+		args = append(args, types.StatusTombstone)
 	}
 
 	if filter.Priority != nil {
diff --git a/internal/types/types.go b/internal/types/types.go
index fdb5e04d..e2e045a5 100644
--- a/internal/types/types.go
+++ b/internal/types/types.go
@@ -297,6 +297,7 @@ type Statistics struct {
 	ClosedIssues             int     `json:"closed_issues"`
 	BlockedIssues            int     `json:"blocked_issues"`
 	ReadyIssues              int     `json:"ready_issues"`
+	TombstoneIssues          int     `json:"tombstone_issues"` // Soft-deleted issues (bd-nyt)
 	EpicsEligibleForClosure  int     `json:"epics_eligible_for_closure"`
 	AverageLeadTime          float64 `json:"average_lead_time_hours"`
 }
@@ -334,6 +335,9 @@ type IssueFilter struct {
 	// Numeric ranges
 	PriorityMin *int
 	PriorityMax *int
+
+	// Tombstone filtering (bd-1bu)
+	IncludeTombstones bool // If false (default), exclude tombstones from results
 }
 
 // SortPolicy determines how ready work is ordered