diff --git a/flow/connectors/external_metadata/store.go b/flow/connectors/external_metadata/store.go
index 3be58019b..93649ffcd 100644
--- a/flow/connectors/external_metadata/store.go
+++ b/flow/connectors/external_metadata/store.go
@@ -139,22 +139,14 @@ func (p *PostgresMetadataStore) SetupMetadata() error {
 			partition_id TEXT NOT NULL,
 			sync_partition JSON NOT NULL,
 			sync_start_time TIMESTAMPTZ NOT NULL,
-			sync_finish_time TIMESTAMPTZ NOT NULL DEFAULT NOW()
+			sync_finish_time TIMESTAMPTZ NOT NULL DEFAULT NOW(),
+			PRIMARY KEY(job_name, partition_id)
 		)`)
 	if err != nil && !utils.IsUniqueError(err) {
 		p.logger.Error("failed to create qrep metadata table", slog.Any("error", err))
 		return err
 	}
 
-	_, err = p.conn.Exec(p.ctx,
-		`CREATE INDEX IF NOT EXISTS ix_qrep_metadata_partition_id ON `+
-			p.QualifyTable(qrepTableName)+
-			` USING hash (partition_id)`)
-	if err != nil && !utils.IsUniqueError(err) {
-		p.logger.Error("failed to create qrep metadata index", slog.Any("error", err))
-		return err
-	}
-
 	p.logger.Info(fmt.Sprintf("created external metadata table %s.%s", p.schemaName, lastSyncStateTableName))
 	return nil
 }
@@ -287,22 +279,23 @@ func (p *PostgresMetadataStore) FinishQrepPartition(
 
 	_, err = p.conn.Exec(p.ctx,
 		`INSERT INTO `+p.QualifyTable(qrepTableName)+
-			`(job_name, partition_id, sync_partition, sync_start_time) VALUES ($1, $2, $3, $4)`,
+			`(job_name, partition_id, sync_partition, sync_start_time) VALUES ($1, $2, $3, $4)
+			ON CONFLICT (job_name, partition_id) DO UPDATE SET sync_partition = $3, sync_start_time = $4, sync_finish_time = NOW()`,
 		jobName, partition.PartitionId, partitionJSON, startTime)
 	return err
 }
 
-func (p *PostgresMetadataStore) IsQrepPartitionSynced(partitionID string) (bool, error) {
-	var count int64
+func (p *PostgresMetadataStore) IsQrepPartitionSynced(jobName string, partitionID string) (bool, error) {
+	var exists bool
 	err := p.conn.QueryRow(p.ctx,
-		`SELECT COUNT(*) FROM `+
+		`SELECT EXISTS(SELECT * FROM `+
 			p.QualifyTable(qrepTableName)+
-			` WHERE partition_id = $1`,
-		partitionID).Scan(&count)
+			` WHERE job_name = $1 AND partition_id = $2)`,
+		jobName, partitionID).Scan(&exists)
 	if err != nil {
 		return false, fmt.Errorf("failed to execute query: %w", err)
 	}
-	return count > 0, nil
+	return exists, nil
 }
 
 func (p *PostgresMetadataStore) DropMetadata(jobName string) error {
diff --git a/flow/connectors/snowflake/qrep.go b/flow/connectors/snowflake/qrep.go
index e3037d298..a5bd38fe0 100644
--- a/flow/connectors/snowflake/qrep.go
+++ b/flow/connectors/snowflake/qrep.go
@@ -33,7 +33,7 @@ func (c *SnowflakeConnector) SyncQRepRecords(
 	}
 	c.logger.Info("Called QRep sync function and obtained table schema", flowLog)
 
-	done, err := c.pgMetadata.IsQrepPartitionSynced(partition.PartitionId)
+	done, err := c.pgMetadata.IsQrepPartitionSynced(config.FlowJobName, partition.PartitionId)
 	if err != nil {
 		return 0, fmt.Errorf("failed to check if partition %s is synced: %w", partition.PartitionId, err)
 	}