diff --git a/pkg/seahorse/short_compaction.go b/pkg/seahorse/short_compaction.go
index 97a0795bb..38676f02f 100644
--- a/pkg/seahorse/short_compaction.go
+++ b/pkg/seahorse/short_compaction.go
@@ -387,13 +387,30 @@ func (e *CompactionEngine) compactCondensed(ctx context.Context, convID int64) (
 
 	startOrd := -1
 	endOrd := -1
+	hasNonCandidate := false
 	for _, item := range items {
 		if item.ItemType == "summary" && candidateSet[item.SummaryID] {
-			if startOrd == -1 || item.Ordinal < startOrd {
-				startOrd = item.Ordinal
-			}
-			if endOrd == -1 || item.Ordinal > endOrd {
-				endOrd = item.Ordinal
+			if startOrd == -1 {
+				startOrd, endOrd = item.Ordinal, item.Ordinal
+			} else {
+				// Check for non-candidate items between endOrd and current ordinal
+				for _, it := range items {
+					if it.Ordinal > endOrd && it.Ordinal <= item.Ordinal {
+						if it.ItemType != "summary" || !candidateSet[it.SummaryID] {
+							hasNonCandidate = true
+							break
+						}
+					}
+				}
+				if hasNonCandidate {
+					break
+				}
+				if item.Ordinal < startOrd {
+					startOrd = item.Ordinal
+				}
+				if item.Ordinal > endOrd {
+					endOrd = item.Ordinal
+				}
 			}
 		}
 	}
@@ -402,8 +419,22 @@ func (e *CompactionEngine) compactCondensed(ctx context.Context, convID int64) (
 		return nil, nil
 	}
 
-	if err := e.store.ReplaceContextRangeWithSummary(ctx, convID, startOrd, endOrd, summary.SummaryID); err != nil {
-		return nil, err
+	// Collect candidate summary IDs
+	candidateIDs := make([]string, 0, len(candidates))
+	for _, c := range candidates {
+		candidateIDs = append(candidateIDs, c.SummaryID)
+	}
+
+	if hasNonCandidate {
+		// Use safe per-item deletion to avoid deleting non-candidate items
+		if err := e.store.ReplaceContextItemsWithSummary(ctx, convID, candidateIDs, summary.SummaryID); err != nil {
+			return nil, err
+		}
+	} else {
+		// Candidates are consecutive, use efficient range deletion
+		if err := e.store.ReplaceContextRangeWithSummary(ctx, convID, startOrd, endOrd, summary.SummaryID); err != nil {
+			return nil, err
+		}
 	}
 
 	return &summary.SummaryID, nil
diff --git a/pkg/seahorse/store.go b/pkg/seahorse/store.go
index 8077f4c75..e50e25d8d 100644
--- a/pkg/seahorse/store.go
+++ b/pkg/seahorse/store.go
@@ -4,7 +4,6 @@ import (
 	"context"
 	"database/sql"
 	"fmt"
-	"strconv"
 	"strings"
 	"time"
 )
@@ -820,6 +819,101 @@ func (s *Store) ReplaceContextRangeWithSummary(
 	return tx.Commit()
 }
 
+// ReplaceContextItemsWithSummary replaces specific context items (by summary_id) with a new summary.
+// Use this when candidates are not contiguous in ordinal space to avoid deleting non-candidate items.
+func (s *Store) ReplaceContextItemsWithSummary(
+	ctx context.Context,
+	convID int64,
+	summaryIDs []string,
+	newSummaryID string,
+) error {
+	if len(summaryIDs) == 0 {
+		return nil
+	}
+
+	tx, err := s.db.BeginTx(ctx, nil)
+	if err != nil {
+		return err
+	}
+	defer tx.Rollback()
+
+	// Find the ordinals of items to delete and calculate midpoint
+	placeholders := make([]string, len(summaryIDs))
+	args := make([]any, len(summaryIDs)+1)
+	args[0] = convID
+	for i, sid := range summaryIDs {
+		placeholders[i] = "?"
+		args[i+1] = sid
+	}
+
+	query := fmt.Sprintf(
+		"SELECT ordinal FROM context_items WHERE conversation_id = ? AND summary_id IN (%s) ORDER BY ordinal",
+		strings.Join(placeholders, ","),
+	)
+	rows, err := tx.QueryContext(ctx, query, args...)
+	if err != nil {
+		return err
+	}
+
+	var ordinals []int
+	for rows.Next() {
+		var ord int
+		if err := rows.Scan(&ord); err != nil {
+			rows.Close()
+			return err
+		}
+		ordinals = append(ordinals, ord)
+	}
+	rows.Close()
+
+	if len(ordinals) == 0 {
+		return nil
+	}
+
+	midpoint := (ordinals[0] + ordinals[len(ordinals)-1]) / 2
+
+	// Delete the specific items by summary_id
+	deleteQuery := fmt.Sprintf(
+		"DELETE FROM context_items WHERE conversation_id = ? AND summary_id IN (%s)",
+		strings.Join(placeholders, ","),
+	)
+	_, err = tx.ExecContext(ctx, deleteQuery, args...)
+	if err != nil {
+		return err
+	}
+
+	// Check if midpoint conflicts with existing ordinal
+	var conflict bool
+	var existingOrd int
+	err = tx.QueryRowContext(ctx,
+		"SELECT ordinal FROM context_items WHERE conversation_id = ? AND ordinal = ?",
+		convID, midpoint,
+	).Scan(&existingOrd)
+	if err == nil {
+		conflict = true
+	}
+
+	if conflict {
+		// Gap exhausted, need resequence
+		err = s.resequenceContextItemsTx(ctx, tx, convID, newSummaryID)
+		if err != nil {
+			return fmt.Errorf("resequence: %w", err)
+		}
+	} else {
+		// Normal insert at midpoint
+		_, err = tx.ExecContext(ctx,
+			`INSERT INTO context_items (conversation_id, ordinal, item_type, summary_id, token_count)
+			 SELECT ?, ?, 'summary', ?, token_count FROM summaries WHERE summary_id = ?`,
+			convID, midpoint, newSummaryID, newSummaryID,
+		)
+		if err != nil {
+			return err
+		}
+	}
+
+	return tx.Commit()
+}
+
 // resequenceContextItemsTx renumbers context_items with fresh OrdinalStep gaps.
 // Uses temp negative ordinals to avoid PRIMARY KEY constraint violations (spec lines 1240-1247).
 func (s *Store) resequenceContextItemsTx(ctx context.Context, tx *sql.Tx, convID int64, newSummaryID string) error {
@@ -844,17 +938,17 @@ func (s *Store) resequenceContextItemsTx(ctx context.Context, tx *sql.Tx, convID
 	var items []item
 	for rows.Next() {
 		var i item
-		var sid, mid sql.NullString
+		var sid sql.NullString
+		var mid sql.NullInt64
 		var scanErr error
 		if scanErr = rows.Scan(&i.ordinal, &i.itemType, &sid, &mid, &i.tokenCount); scanErr != nil {
-			return err
+			return scanErr
 		}
 		if sid.Valid {
 			i.summaryID = sid.String
 		}
 		if mid.Valid {
-			id, _ := strconv.ParseInt(mid.String, 10, 64)
-			i.messageID = id
+			i.messageID = mid.Int64
 		}
 		items = append(items, i)
 	}
diff --git a/pkg/seahorse/store_test.go b/pkg/seahorse/store_test.go
index 22790ebdc..3dca90a89 100644
--- a/pkg/seahorse/store_test.go
+++ b/pkg/seahorse/store_test.go
@@ -1141,3 +1141,107 @@ func TestStoreSearchSummariesReturnsContent(t *testing.T) {
 		t.Errorf("SearchResult.Content = %q, want %q", results[0].Content, "This is the summary content for testing")
 	}
 }
+
+func TestStoreReplaceContextItemsWithSummary(t *testing.T) {
+	s := openTestStore(t)
+	ctx := context.Background()
+
+	conv, _ := s.GetOrCreateConversation(ctx, "agent:test-replace-items")
+
+	// Create messages
+	msgs := make([]int64, 5)
+	for i := 0; i < 5; i++ {
+		m, _ := s.AddMessage(ctx, conv.ConversationID, "user", fmt.Sprintf("msg%d", i), 2)
+		msgs[i] = m.ID
+	}
+
+	// Create summaries
+	summaries := make([]string, 3)
+	for i := 0; i < 3; i++ {
+		sum, _ := s.CreateSummary(ctx, CreateSummaryInput{
+			ConversationID: conv.ConversationID,
+			Kind:           SummaryKindLeaf,
+			Depth:          0,
+			Content:        fmt.Sprintf("summary %d", i),
+			TokenCount:     10,
+		})
+		summaries[i] = sum.SummaryID
+	}
+
+	// Insert context items with a message in between summaries:
+	// Ordinals: 100 (summary0), 200 (message), 300 (summary1), 400 (summary2)
+	items := []ContextItem{
+		{Ordinal: 100, ItemType: "summary", SummaryID: summaries[0], TokenCount: 10},
+		{Ordinal: 200, ItemType: "message", MessageID: msgs[1], TokenCount: 2},
+		{Ordinal: 300, ItemType: "summary", SummaryID: summaries[1], TokenCount: 10},
+		{Ordinal: 400, ItemType: "summary", SummaryID: summaries[2], TokenCount: 10},
+	}
+	s.UpsertContextItems(ctx, conv.ConversationID, items)
+
+	// Create a new summary to replace with
+	newSummary, _ := s.CreateSummary(ctx, CreateSummaryInput{
+		ConversationID: conv.ConversationID,
+		Kind:           SummaryKindCondensed,
+		Depth:          1,
+		Content:        "condensed summary",
+		TokenCount:     15,
+	})
+
+	// Replace summaries 0 and 1 (not 2) using per-item deletion
+	// This should NOT delete the message at ordinal 200
+	err := s.ReplaceContextItemsWithSummary(ctx, conv.ConversationID, []string{summaries[0], summaries[1]}, newSummary.SummaryID)
+	if err != nil {
+		t.Fatalf("ReplaceContextItemsWithSummary: %v", err)
+	}
+
+	// Verify result: should have 3 items (message at 200, summary2 at 400, new summary)
+	result, _ := s.GetContextItems(ctx, conv.ConversationID)
+	if len(result) != 3 {
+		t.Fatalf("expected 3 items after replace, got %d", len(result))
+	}
+
+	// Verify message at ordinal 200 is preserved
+	messagePreserved := false
+	for _, item := range result {
+		if item.ItemType == "message" && item.MessageID == msgs[1] {
+			messagePreserved = true
+			break
+		}
+	}
+	if !messagePreserved {
+		t.Error("message at ordinal 200 should have been preserved")
+	}
+
+	// Verify summary2 at ordinal 400 is preserved
+	summary2Preserved := false
+	for _, item := range result {
+		if item.ItemType == "summary" && item.SummaryID == summaries[2] {
+			summary2Preserved = true
+			break
+		}
+	}
+	if !summary2Preserved {
+		t.Error("summary2 at ordinal 400 should have been preserved")
+	}
+
+	// Verify new summary exists
+	newSummaryFound := false
+	for _, item := range result {
+		if item.ItemType == "summary" && item.SummaryID == newSummary.SummaryID {
+			newSummaryFound = true
+			break
+		}
+	}
+	if !newSummaryFound {
+		t.Error("new summary should exist")
+	}
+
+	// Verify no duplicate ordinals
+	ordinalSet := make(map[int]bool)
+	for _, item := range result {
+		if ordinalSet[item.Ordinal] {
+			t.Errorf("duplicate ordinal %d detected", item.Ordinal)
+		}
+		ordinalSet[item.Ordinal] = true
+	}
+}