diff --git a/dgraph/cmd/root.go b/dgraph/cmd/root.go
index 233295bca01..3f995973715 100644
--- a/dgraph/cmd/root.go
+++ b/dgraph/cmd/root.go
@@ -84,7 +84,8 @@ var rootConf = viper.New()
 // subcommands initially contains all default sub-commands.
 var subcommands = []*x.SubCommand{
 	&bulk.Bulk, &cert.Cert, &conv.Conv, &live.Live, &alpha.Alpha, &zero.Zero, &version.Version,
-	&debug.Debug, &migrate.Migrate, &debuginfo.DebugInfo, &upgrade.Upgrade, &decrypt.Decrypt, &increment.Increment,
+	&debug.Debug, &migrate.Migrate, &debuginfo.DebugInfo, &upgrade.Upgrade, &decrypt.Decrypt,
+	&increment.Increment,
 }
 
 func initCmds() {
diff --git a/dgraph/cmd/root_ee.go b/dgraph/cmd/root_ee.go
index 70c2a7d8b5f..80f5591eca5 100644
--- a/dgraph/cmd/root_ee.go
+++ b/dgraph/cmd/root_ee.go
@@ -16,6 +16,7 @@ import (
 	acl "github.com/dgraph-io/dgraph/ee/acl"
 	"github.com/dgraph-io/dgraph/ee/audit"
 	"github.com/dgraph-io/dgraph/ee/backup"
+	"github.com/dgraph-io/dgraph/ee/updatemanifest"
 )
 
 func init() {
@@ -25,5 +26,6 @@ func init() {
 		&backup.ExportBackup,
 		&acl.CmdAcl,
 		&audit.CmdAudit,
+		&updatemanifest.UpdateManifest,
 	)
 }
diff --git a/ee/updatemanifest/run.go b/ee/updatemanifest/run.go
new file mode 100644
index 00000000000..3f605d08547
--- /dev/null
+++ b/ee/updatemanifest/run.go
@@ -0,0 +1,127 @@
+// +build !oss
+
+/*
+ * Copyright 2021 Dgraph Labs, Inc. and Contributors
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package updatemanifest
+
+import (
+	"encoding/binary"
+	"log"
+	"net/url"
+	"os"
+	"strings"
+
+	"github.com/dgraph-io/dgraph/ee"
+	"github.com/dgraph-io/dgraph/protos/pb"
+	"github.com/dgraph-io/dgraph/worker"
+	"github.com/dgraph-io/dgraph/x"
+	"github.com/pkg/errors"
+	"github.com/spf13/cobra"
+)
+
+var (
+	logger = log.New(os.Stderr, "", 0)
+	// UpdateManifest is the sub-command invoked when running "dgraph update_manifest".
+	UpdateManifest x.SubCommand
+)
+
+var opt struct {
+	location string
+	key      []byte
+}
+
+func init() {
+	UpdateManifest.Cmd = &cobra.Command{
+		Use:   "update_manifest",
+		Short: "Run the Dgraph update tool to update the manifest from v21.03 to latest.",
+		Run: func(cmd *cobra.Command, args []string) {
+			if err := run(); err != nil {
+				logger.Fatalf("%v\n", err)
+			}
+		},
+		Annotations: map[string]string{"group": "tool"},
+	}
+	UpdateManifest.EnvPrefix = "DGRAPH_UPDATE_MANIFEST"
+	UpdateManifest.Cmd.SetHelpTemplate(x.NonRootTemplate)
+
+	flag := UpdateManifest.Cmd.Flags()
+	flag.StringVarP(&opt.location, "location", "l", "",
+		`Sets the location of the backup. Both file URIs and s3 are supported.
+		This command will take care of all the full + incremental backups present in the location.`)
+	ee.RegisterEncFlag(flag)
+}
+
+// Invalid bytes are replaced with the Unicode replacement rune.
+// See https://golang.org/pkg/encoding/json/#Marshal
+const replacementRune = rune('\ufffd')
+
+func parseNsAttr(attr string) (uint64, string, error) {
+	if strings.ContainsRune(attr, replacementRune) {
+		return 0, "", errors.New("replacement char found")
+	}
+	return binary.BigEndian.Uint64([]byte(attr[:8])), attr[8:], nil
+}
+
+func run() error {
+	keys, err := ee.GetKeys(UpdateManifest.Conf)
+	if err != nil {
+		return err
+	}
+	opt.key = keys.EncKey
+	uri, err := url.Parse(opt.location)
+	if err != nil {
+		return errors.Wrapf(err, "while parsing location")
+	}
+	handler, err := worker.NewUriHandler(uri, nil)
+	if err != nil {
+		return errors.Wrapf(err, "while creating uri handler")
+	}
+	masterManifest, err := worker.GetManifest(handler, uri)
+	if err != nil {
+		return errors.Wrapf(err, "while getting manifest")
+	}
+
+	// Update the master manifest with the changes for drop operations and group predicates.
+	for _, manifest := range masterManifest.Manifests {
+		for gid, preds := range manifest.Groups {
+			parsedPreds := preds[:0]
+			for _, pred := range preds {
+				ns, attr, err := parseNsAttr(pred)
+				if err != nil {
+					logger.Printf("Unable to parse the pred: %v", pred)
+					continue
+				}
+				parsedPreds = append(parsedPreds, x.NamespaceAttr(ns, attr))
+			}
+			manifest.Groups[gid] = parsedPreds
+		}
+		for _, op := range manifest.DropOperations {
+			if op.DropOp == pb.DropOperation_ATTR {
+				ns, attr, err := parseNsAttr(op.DropValue)
+				if err != nil {
+					logger.Printf("Unable to parse the drop operation %+v pred: %v",
+						op, []byte(op.DropValue))
+					continue
+				}
+				op.DropValue = x.NamespaceAttr(ns, attr)
+			}
+		}
+	}
+
+	// Rewrite the master manifest.
+	return errors.Wrap(worker.CreateManifest(handler, uri, masterManifest), "rewrite failed")
+}
diff --git a/worker/backup_ee.go b/worker/backup_ee.go
index e5fda2a8d39..f787527c765 100644
--- a/worker/backup_ee.go
+++ b/worker/backup_ee.go
@@ -573,7 +573,7 @@ func (pr *BackupProcessor) CompleteBackup(ctx context.Context, m *Manifest) erro
 	}
 	manifest.Manifests = append(manifest.Manifests, m)
 
-	if err := createManifest(handler, uri, manifest); err != nil {
+	if err := CreateManifest(handler, uri, manifest); err != nil {
 		return errors.Wrap(err, "Complete backup failed")
 	}
 	glog.Infof("Backup completed OK.")
@@ -687,7 +687,7 @@ func checkAndGetDropOp(key []byte, l *posting.List, readTs uint64) (*pb.DropOper
 		// * DROP_NS;ns
 		// So, accordingly construct the *pb.DropOperation.
 		dropOp := &pb.DropOperation{}
-		dropInfo := strings.Split(string(val), ";")
+		dropInfo := strings.SplitN(string(val), ";", 2)
 		if len(dropInfo) != 2 {
 			return nil, errors.Errorf("Unexpected value: %s for dgraph.drop.op", val)
 		}
diff --git a/worker/backup_manifest.go b/worker/backup_manifest.go
index fa1682bba6e..3797221243e 100644
--- a/worker/backup_manifest.go
+++ b/worker/backup_manifest.go
@@ -134,7 +134,7 @@ func getFilteredManifests(h x.UriHandler, manifests []*Manifest,
 	for _, m := range manifests {
 		missingFiles := false
 		for g := range m.Groups {
-			path := filepath.Join(m.Path, backupName(m.Since, g))
+			path := filepath.Join(m.Path, backupName(m.ValidReadTs(), g))
 			if !h.FileExists(path) {
 				missingFiles = true
 				break
@@ -244,7 +244,7 @@ func GetManifest(h x.UriHandler, uri *url.URL) (*MasterManifest, error) {
 	return manifest, nil
 }
 
-func createManifest(h x.UriHandler, uri *url.URL, manifest *MasterManifest) error {
+func CreateManifest(h x.UriHandler, uri *url.URL, manifest *MasterManifest) error {
 	var err error
 	if !h.DirExists("./") {
 		if err := h.CreateDir("./"); err != nil {