diff --git a/cmd/backscroll/mixed_provider_e2e_test.go b/cmd/backscroll/mixed_provider_e2e_test.go
index c4acecf..d85024a 100644
--- a/cmd/backscroll/mixed_provider_e2e_test.go
+++ b/cmd/backscroll/mixed_provider_e2e_test.go
@@ -1,10 +1,12 @@
 package main
 
 import (
+	"bytes"
 	"database/sql"
 	"encoding/json"
 	"fmt"
 	"os"
+	"os/exec"
 	"path/filepath"
 	"reflect"
 	"strings"
@@ -197,7 +199,39 @@ func TestMixedProviderNativeOwnershipReplayAndRecovery(t *testing.T) {
 	available.run("rebuild")
 	equal(query(available.database, snapshot), stable)
 	equal(query(available.database, outcomes), signals)
-	for _, path := range []string{omp, pi, codex, oc} {
+	// A mixed sync keeps perennial records from both orphaned native groups
+	// and an expired filesystem capability.
+	if err := os.Remove(omp); err != nil {
+		t.Fatal(err)
+	}
+	native, err = sql.Open("sqlite", oc)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if _, err := native.Exec(`DELETE FROM session WHERE id='s0'`); err != nil {
+		t.Fatal(err)
+	}
+	if err := native.Close(); err != nil {
+		t.Fatal(err)
+	}
+	cmd := exec.Command(e.binary, "search", "--text", "mixedproviderquartz", "--all-projects", "--json")
+	cmd.Dir, cmd.Env = e.root, e.environment
+	var stderr bytes.Buffer
+	cmd.Stderr = &stderr
+	output, err := cmd.Output()
+	if err != nil {
+		t.Fatalf("mixed orphan sync: %v stderr=%s", err, &stderr)
+	}
+	if strings.Count(stderr.String(), "warning: opencode: skipped 1 messages without native session metadata\n") != 1 {
+		t.Fatalf("orphan warning: %s", &stderr)
+	}
+	var retained []json.RawMessage
+	if err := json.Unmarshal(output, &retained); err != nil || len(retained) != 5 {
+		t.Fatalf("stdout JSON: %s err=%v", output, err)
+	}
+	equal(query(e.database, snapshot), stable)
+	equal(query(e.database, outcomes), signals)
+	for _, path := range []string{pi, codex, oc} {
 		if err := os.Remove(path); err != nil {
 			t.Fatal(err)
 		}
diff --git a/cmd/backscroll/startup_policy.go b/cmd/backscroll/startup_policy.go
index 607a8ea..fb34594 100644
--- a/cmd/backscroll/startup_policy.go
+++ b/cmd/backscroll/startup_policy.go
@@ -252,6 +252,7 @@ query merges both by rank position (RRF).`,
 				return nil
 			}
 			ctx := cmd.Context()
+			ctx = context.WithValue(ctx, startupWarningWriterKey{}, stderr)
 			if syncService.diagnostics {
 				ctx = context.WithValue(ctx, startupDiagnosticsWriterKey{}, stderr)
 			}
diff --git a/cmd/backscroll/sync_helpers.go b/cmd/backscroll/sync_helpers.go
index d538bf8..bcb07b4 100644
--- a/cmd/backscroll/sync_helpers.go
+++ b/cmd/backscroll/sync_helpers.go
@@ -390,6 +390,8 @@ func isRacyCleanFile(fileMtime string, lastIndexed string) bool {
 	return fileMt.After(indexTime.Add(-time.Duration(racyMarginSeconds) * time.Second))
 }
 
+type startupWarningWriterKey struct{}
+
 // maybeAutoSync preserves the legacy non-cancellable entry point by creating
 // production dependencies for this invocation rather than using shared state.
 func maybeAutoSync(cfg *config.Config, progress io.Writer) error {
@@ -644,6 +646,7 @@ func (s *startupSyncService) syncWithProgress(ctx context.Context, cfg *config.C
 	// selected replays are deterministic even when discovery order changes.
 	var indexedFiles []storage.IndexedFile
 	semanticsReplaysDone, staleReplaysDone := 0, 0
+	skippedOpenCodeMessages := 0
 	for _, claim := range uniqueClaims {
 		if err := ctx.Err(); err != nil {
 			return err
@@ -671,6 +674,9 @@ func (s *startupSyncService) syncWithProgress(ctx context.Context, cfg *config.C
 		if err != nil {
 			return fmt.Errorf("parse %s: %w", ref, err)
 		}
+		if reader.Name() == "opencode" {
+			skippedOpenCodeMessages += pf.SkippedMessages
+		}
 		if err := ctx.Err(); err != nil {
 			return err
 		}
@@ -821,5 +827,13 @@ func (s *startupSyncService) syncWithProgress(ctx context.Context, cfg *config.C
 		return err
 	}
 
+	if skippedOpenCodeMessages > 0 {
+		warnings, ok := ctx.Value(startupWarningWriterKey{}).(io.Writer)
+		if !ok {
+			warnings = progress
+		}
+		_, _ = fmt.Fprintf(warnings, "warning: opencode: skipped %d messages without native session metadata\n", skippedOpenCodeMessages)
+	}
+
 	return nil
 }
diff --git a/docs/input-contract.md b/docs/input-contract.md
index 3057195..cb1320e 100644
--- a/docs/input-contract.md
+++ b/docs/input-contract.md
@@ -617,10 +617,15 @@ A single SQLite capability remains one `source_path`; it can contain many native
 sessions. Each indexed record carries the structured `message.session_id` and,
 when available, the joined `session.directory`. A present directory is used for
 project-registry identification. When native cwd is absent, project proof remains
-unknown; the database location supplies no native project attribution. Missing rows in a present
-session table, empty identities, contradictory message/part session IDs, and
-relative or NUL-bearing directories fail the parse conservatively. Message/part-only
-exports remain supported without inventing native cwd.
+unknown; the database location supplies no native project attribution. When the
+session table exists, messages with a matching native session row and their parts
+are eligible for indexing. Messages whose native session row is missing are
+skipped together with their parts, counted once per message, and reported on
+stderr during startup sync. Previously indexed native records retain their
+payloads and anchors. Empty identities, contradictory message/part session IDs,
+parts without a message row, and relative or NUL-bearing directories fail the
+parse conservatively. Message/part-only exports remain supported without
+inventing native cwd.
 
 Text identity is a deterministic UUIDv5 over a namespace-qualified native message
 ID. Tool identity is a deterministic UUIDv5 over native message and part IDs, with
diff --git a/internal/models/models.go b/internal/models/models.go
index c598121..d5c68b4 100644
--- a/internal/models/models.go
+++ b/internal/models/models.go
@@ -26,10 +26,11 @@ type SearchResult struct {
 
 // ParsedFile represents a parsed session or plan file.
 type ParsedFile struct {
-	Path    string
-	Hash    string // SHA-256 hex
-	Records []Message
-	Cwd     string // working directory, used for project identification
+	Path            string
+	Hash            string // SHA-256 hex
+	Records         []Message
+	Cwd             string // working directory, used for project identification
+	SkippedMessages int    // messages skipped because native session metadata is unavailable
 }
 
 // Message represents a message in a session.
diff --git a/internal/readers/opencode_native_test.go b/internal/readers/opencode_native_test.go
index e550b65..28b8f1e 100644
--- a/internal/readers/opencode_native_test.go
+++ b/internal/readers/opencode_native_test.go
@@ -115,8 +115,9 @@ func TestOpenCodeNativeToolIdentityAndMalformedMetadata(t *testing.T) {
 	if _, err := db.Exec(`DELETE FROM session`); err != nil {
 		t.Fatal(err)
 	}
-	if _, err := reader.Parse(context.Background(), path, input_config.InputDefinition{}); err == nil {
-		t.Fatal("orphan session silently fell back")
+	orphaned, err := reader.Parse(context.Background(), path, input_config.InputDefinition{})
+	if err != nil || len(orphaned.Records) != 0 || orphaned.SkippedMessages != 4 {
+		t.Fatalf("orphan groups: %+v err=%v", orphaned, err)
 	}
 }
 
diff --git a/internal/readers/opencode_reader.go b/internal/readers/opencode_reader.go
index e0765db..4c3d315 100644
--- a/internal/readers/opencode_reader.go
+++ b/internal/readers/opencode_reader.go
@@ -174,13 +174,11 @@ func parseOpenCodeSnapshot(ctx context.Context, tx *sql.Tx, dbPath string) (mode
 	if invalid {
 		return models.ParsedFile{}, fmt.Errorf("invalid OpenCode message/part relationship")
 	}
+	var skippedMessages int
 	if hasSession {
-		if err := tx.QueryRowContext(ctx, `SELECT EXISTS(SELECT 1 FROM message m LEFT JOIN session s ON s.id=m.session_id WHERE s.id IS NULL)`).Scan(&invalid); err != nil {
+		if err := tx.QueryRowContext(ctx, `SELECT COUNT(*) FROM message m LEFT JOIN session s ON s.id=m.session_id WHERE s.id IS NULL`).Scan(&skippedMessages); err != nil {
 			return models.ParsedFile{}, err
 		}
-		if invalid {
-			return models.ParsedFile{}, fmt.Errorf("OpenCode message has no native session metadata")
-		}
 	}
 	directory, join, sessionColumn := "NULL", "", "NULL"
 	if hasSession {
@@ -253,12 +251,12 @@ func parseOpenCodeSnapshot(ctx context.Context, tx *sql.Tx, dbPath string) (mode
 			return models.ParsedFile{}, err
 		}
 
-		if hasSession && !nativeSession.Valid {
-			return models.ParsedFile{}, fmt.Errorf("OpenCode message has no native session metadata")
-		}
 		if !validOpenCodeID(msgID) || !validOpenCodeID(partID) || !validOpenCodeID(sessionID) || partSession != sessionID {
 			return models.ParsedFile{}, fmt.Errorf("invalid OpenCode native identity or session relationship")
 		}
+		if hasSession && !nativeSession.Valid {
+			continue
+		}
 		if cwd.Valid && cwd.String != "" && (!filepath.IsAbs(cwd.String) || strings.IndexByte(cwd.String, 0) >= 0) {
 			return models.ParsedFile{}, fmt.Errorf("invalid OpenCode native directory")
 		}
@@ -317,9 +315,10 @@ func parseOpenCodeSnapshot(ctx context.Context, tx *sql.Tx, dbPath string) (mode
 	}
 
 	return models.ParsedFile{
-		Path:    dbPath,
-		Hash:    hash,
-		Records: msgs,
+		Path:            dbPath,
+		Hash:            hash,
+		Records:         msgs,
+		SkippedMessages: skippedMessages,
 	}, nil
 }
 
diff --git a/internal/readers/opencode_snapshot_test.go b/internal/readers/opencode_snapshot_test.go
index 8494041..0e997f0 100644
--- a/internal/readers/opencode_snapshot_test.go
+++ b/internal/readers/opencode_snapshot_test.go
@@ -149,3 +149,42 @@ func TestOpenCodeSnapshotCancellation(t *testing.T) {
 		t.Fatal("Parse ignored cancellation")
 	}
 }
+
+func TestOpenCodeSnapshotSkipsMissingSessionGroups(t *testing.T) {
+	path := createOpenCodeDB(t)
+	db, err := sql.Open("sqlite", path)
+	if err != nil {
+		t.Fatal(err)
+	}
+	defer db.Close()
+	if _, err := db.Exec(`CREATE TABLE session(id TEXT PRIMARY KEY,directory TEXT); INSERT INTO session VALUES('sess-1','/projects/native')`); err != nil {
+		t.Fatal(err)
+	}
+	reader := &OpenCodeReader{}
+	before, err := reader.Parse(context.Background(), path, input_config.InputDefinition{})
+	if err != nil {
+		t.Fatal(err)
+	}
+	if _, err := db.Exec(`INSERT INTO message VALUES('orphan-a','missing',0,0,'{"role":"user"}'),('orphan-b','missing',0,0,'{"role":"assistant"}'),('orphan-empty','missing',0,0,'{"role":"user"}'); INSERT INTO part VALUES('orphan-p1','orphan-a','missing',0,0,'{"type":"text","text":"orphan"}'),('orphan-p2','orphan-a','missing',0,0,'{"type":"text","text":"also orphan"}'),('orphan-p3','orphan-b','missing',0,0,'{"type":"tool","tool":"Bash","state":{"input":{"command":"echo orphan"},"output":"orphan"}}')`); err != nil {
+		t.Fatal(err)
+	}
+	after, err := reader.Parse(context.Background(), path, input_config.InputDefinition{})
+	if err != nil {
+		t.Fatal(err)
+	}
+	if after.SkippedMessages != 3 || len(after.Records) != len(before.Records) {
+		t.Fatalf("skipped groups: %+v", after)
+	}
+	for i, message := range after.Records {
+		want := before.Records[i]
+		if message != want || message.UUID == "" || message.SessionID != "sess-1" || message.Cwd != "/projects/native" || message.Origin == "" {
+			t.Fatalf("native record changed: %+v want %+v", message, want)
+		}
+	}
+	if _, err := db.Exec(`INSERT INTO part VALUES('broken','absent-message','missing',0,0,'{"type":"text","text":"broken"}')`); err != nil {
+		t.Fatal(err)
+	}
+	if _, err := reader.Parse(context.Background(), path, input_config.InputDefinition{}); err == nil || err.Error() != "invalid OpenCode message/part relationship" {
+		t.Fatalf("relationship error: %v", err)
+	}
+}