diff --git a/dm/syncer/syncer.go b/dm/syncer/syncer.go
index 94f6fa8777a..c158bcfb4f2 100644
--- a/dm/syncer/syncer.go
+++ b/dm/syncer/syncer.go
@@ -38,6 +38,13 @@ import (
 	"github.com/pingcap/tidb/parser/format"
 	"github.com/pingcap/tidb/parser/model"
 	"github.com/pingcap/tidb/sessionctx"
+<<<<<<< HEAD
+=======
+	"github.com/pingcap/tidb/util/dbutil"
+	"github.com/pingcap/tidb/util/filter"
+	regexprrouter "github.com/pingcap/tidb/util/regexpr-router"
+	router "github.com/pingcap/tidb/util/table-router"
+>>>>>>> cd9032152 (syncer(dm): fix failed row skipped due to incorrect checkpoint flush (#5295))
 	clientv3 "go.etcd.io/etcd/client/v3"
 	"go.uber.org/atomic"
 	"go.uber.org/zap"
@@ -1011,8 +1018,7 @@ func (s *Syncer) checkShouldFlush() error {
 		s.flushCheckPointsAsync(j)
 		return nil
 	}
-	s.jobWg.Wait()
-	return s.flushCheckPoints()
+	return s.flushJobs()
 }
 
 // TODO: move to syncer/job.go
diff --git a/dm/tests/tracker_ignored_ddl/conf/dm-task.yaml b/dm/tests/tracker_ignored_ddl/conf/dm-task.yaml
index a1dc02ebc87..4a54be354d5 100644
--- a/dm/tests/tracker_ignored_ddl/conf/dm-task.yaml
+++ b/dm/tests/tracker_ignored_ddl/conf/dm-task.yaml
@@ -46,3 +46,4 @@ syncers:
     worker-count: 16
     batch: 100
     enable-ansi-quotes: false  # compatible with deprecated config
+    checkpoint-flush-interval: 1
diff --git a/dm/tests/tracker_ignored_ddl/conf/source1.yaml b/dm/tests/tracker_ignored_ddl/conf/source1_gtid.yaml
similarity index 100%
rename from dm/tests/tracker_ignored_ddl/conf/source1.yaml
rename to dm/tests/tracker_ignored_ddl/conf/source1_gtid.yaml
diff --git a/dm/tests/tracker_ignored_ddl/conf/source1_pos.yaml b/dm/tests/tracker_ignored_ddl/conf/source1_pos.yaml
new file mode 100644
index 00000000000..7d67feb8cfd
--- /dev/null
+++ b/dm/tests/tracker_ignored_ddl/conf/source1_pos.yaml
@@ -0,0 +1,11 @@
+source-id: mysql-replica-01
+flavor: ''
+enable-gtid: false
+enable-relay: true
+relay-binlog-name: ''
+relay-binlog-gtid: ''
+from:
+  host: 127.0.0.1
+  user: root
+  password: /Q7B9DizNLLTTfiZHv9WoEAKamfpIUs=
+  port: 3306
diff --git a/dm/tests/tracker_ignored_ddl/run.sh b/dm/tests/tracker_ignored_ddl/run.sh
index 670eadd4337..a26ca8e206f 100644
--- a/dm/tests/tracker_ignored_ddl/run.sh
+++ b/dm/tests/tracker_ignored_ddl/run.sh
@@ -7,6 +7,7 @@ source $cur/../_utils/test_prepare
 WORK_DIR=$TEST_DIR/$TEST_NAME
 
 function run() {
+	source_cfg=$1
 	run_sql_file $cur/data/db.prepare.sql $MYSQL_HOST1 $MYSQL_PORT1 $MYSQL_PASSWORD1
 
 	run_dm_master $WORK_DIR/master $MASTER_PORT $cur/conf/dm-master.toml
@@ -14,7 +15,7 @@ function run() {
 	run_dm_worker $WORK_DIR/worker1 $WORKER1_PORT $cur/conf/dm-worker.toml
 	check_rpc_alive $cur/../bin/check_worker_online 127.0.0.1:$WORKER1_PORT
 	# operate mysql config to worker
-	cp $cur/conf/source1.yaml $WORK_DIR/source1.yaml
+	cp $cur/conf/$source_cfg $WORK_DIR/source1.yaml
 	dmctl_operate_source create $WORK_DIR/source1.yaml $SOURCE_ID1
 
 	# start DM task only
@@ -27,6 +28,14 @@ function run() {
 	check_not_contains "ignore_1"
 	echo "increment1 check success"
 
+<<<<<<< HEAD
+=======
+	# a not ignored DDL to trigger a checkpoint flush
+	run_sql_source1 "create table tracker_ignored_ddl.test (c int primary key);"
+
+	# sleep 2 second, so the next insert will trigger check point flush since checkpoint-flush-interval=1
+	sleep 2
+>>>>>>> cd9032152 (syncer(dm): fix failed row skipped due to incorrect checkpoint flush (#5295))
 	run_sql_file $cur/data/db.increment2.sql $MYSQL_HOST1 $MYSQL_PORT1 $MYSQL_PASSWORD1
 	run_dm_ctl_with_retry $WORK_DIR "127.0.0.1:$MASTER_PORT" \
 		"query-status test" \
@@ -55,12 +64,18 @@ function run() {
 	run_dm_ctl_with_retry $WORK_DIR "127.0.0.1:$MASTER_PORT" \
 		"query-status test" \
 		"\"stage\": \"Running\"" 1
+
+	run_dm_ctl $WORK_DIR "127.0.0.1:$MASTER_PORT" \
+		"stop-task test" \
+		"\"result\": true" 2
+	dmctl_operate_source stop $WORK_DIR/source1.yaml $SOURCE_ID1
 }
 
 cleanup_data $TEST_NAME
 # also cleanup dm processes in case of last run failed
 cleanup_process
-run
+run source1_gtid.yaml
+run source1_pos.yaml
 cleanup_process
 
 echo "[$(date)] <<<<<< test case $TEST_NAME success! >>>>>>"