diff --git a/weed/shell/command_volume_check_disk.go b/weed/shell/command_volume_check_disk.go
index 41c28b810..6a1634f8a 100644
--- a/weed/shell/command_volume_check_disk.go
+++ b/weed/shell/command_volume_check_disk.go
@@ -13,6 +13,7 @@ import (
 	"google.golang.org/grpc"
 	"io"
 	"math"
+	"net/http"
 	"time"
 )
 
@@ -21,7 +22,8 @@ func init() {
 }
 
 type commandVolumeCheckDisk struct {
-	env *CommandEnv
+	env           *CommandEnv
+	syncDeletions *bool
 }
 
 func (c *commandVolumeCheckDisk) Name() string {
@@ -49,6 +51,7 @@ func (c *commandVolumeCheckDisk) Do(args []string, commandEnv *CommandEnv, write
 	verbose := fsckCommand.Bool("v", false, "verbose mode")
 	volumeId := fsckCommand.Uint("volumeId", 0, "the volume id")
 	applyChanges := fsckCommand.Bool("force", false, "apply the fix")
+	c.syncDeletions = fsckCommand.Bool("syncDeleted", false, "sync of deletions the fix")
 	nonRepairThreshold := fsckCommand.Float64("nonRepairThreshold", 0.3, "repair when missing keys is not more than this limit")
 	if err = fsckCommand.Parse(args); err != nil {
 		return nil
@@ -145,13 +148,17 @@ func (c *commandVolumeCheckDisk) doVolumeCheckDisk(minuend, subtrahend *needle_m
 	// find missing keys
 	// hash join, can be more efficient
 	var missingNeedles []needle_map.NeedleValue
+	var partiallyDeletedNeedles []needle_map.NeedleValue
 	var counter int
 	doCutoffOfLastNeedle := true
-	minuend.DescendingVisit(func(value needle_map.NeedleValue) error {
+	minuend.DescendingVisit(func(minuendValue needle_map.NeedleValue) error {
 		counter++
-		if _, found := subtrahend.Get(value.Key); !found {
+		if subtrahendValue, found := subtrahend.Get(minuendValue.Key); !found {
+			if minuendValue.Size.IsDeleted() {
+				return nil
+			}
 			if doCutoffOfLastNeedle {
-				if needleMeta, err := readNeedleMeta(c.env.option.GrpcDialOption, pb.NewServerAddressFromDataNode(source.location.dataNode), source.info.Id, value); err == nil {
+				if needleMeta, err := readNeedleMeta(c.env.option.GrpcDialOption, pb.NewServerAddressFromDataNode(source.location.dataNode), source.info.Id, minuendValue); err == nil {
 					// needles older than the cutoff time are not missing yet
 					if needleMeta.AppendAtNs > cutoffFromAtNs {
 						return nil
@@ -159,16 +166,22 @@ func (c *commandVolumeCheckDisk) doVolumeCheckDisk(minuend, subtrahend *needle_m
 					doCutoffOfLastNeedle = false
 				}
 			}
-			missingNeedles = append(missingNeedles, value)
-		} else if doCutoffOfLastNeedle {
-			doCutoffOfLastNeedle = false
+			missingNeedles = append(missingNeedles, minuendValue)
+		} else {
+			if minuendValue.Size.IsDeleted() && !subtrahendValue.Size.IsDeleted() {
+				partiallyDeletedNeedles = append(partiallyDeletedNeedles, minuendValue)
+			}
+			if doCutoffOfLastNeedle {
+				doCutoffOfLastNeedle = false
+			}
 		}
 		return nil
 	})
 
-	fmt.Fprintf(writer, "volume %d %s has %d entries, %s missed %d entries\n", source.info.Id, source.location.dataNode.Id, counter, target.location.dataNode.Id, len(missingNeedles))
+	fmt.Fprintf(writer, "volume %d %s has %d entries, %s missed %d and partially deleted %d entries\n",
+		source.info.Id, source.location.dataNode.Id, counter, target.location.dataNode.Id, len(missingNeedles), len(partiallyDeletedNeedles))
 
-	if counter == 0 || len(missingNeedles) == 0 {
+	if counter == 0 || (len(missingNeedles) == 0 && len(partiallyDeletedNeedles) == 0) {
 		return false, nil
 	}
 
@@ -190,7 +203,7 @@ func (c *commandVolumeCheckDisk) doVolumeCheckDisk(minuend, subtrahend *needle_m
 		}
 
 		if verbose {
-			fmt.Fprintf(writer, "read %d,%x %s => %s \n", source.info.Id, needleValue.Key, source.location.dataNode.Id, target.location.dataNode.Id)
+			fmt.Fprintf(writer, "read %s %s => %s\n", needleValue.Key.FileId(source.info.Id), source.location.dataNode.Id, target.location.dataNode.Id)
 		}
 
 		hasChanges = true
@@ -201,6 +214,27 @@ func (c *commandVolumeCheckDisk) doVolumeCheckDisk(minuend, subtrahend *needle_m
 
 	}
 
+	if *c.syncDeletions && len(partiallyDeletedNeedles) > 0 {
+		var fidList []string
+		for _, needleValue := range partiallyDeletedNeedles {
+			fidList = append(fidList, needleValue.Key.FileId(source.info.Id))
+			if verbose {
+				fmt.Fprintf(writer, "delete %s %s => %s\n", needleValue.Key.FileId(source.info.Id), source.location.dataNode.Id, target.location.dataNode.Id)
+			}
+		}
+		deleteResults, deleteErr := operation.DeleteFilesAtOneVolumeServer(
+			pb.NewServerAddressFromDataNode(target.location.dataNode),
+			c.env.option.GrpcDialOption, fidList, false)
+		if deleteErr != nil {
+			return hasChanges, deleteErr
+		}
+		for _, deleteResult := range deleteResults {
+			if deleteResult.Status == http.StatusAccepted {
+				hasChanges = true
+				return
+			}
+		}
+	}
 	return
 }
 
@@ -245,9 +279,7 @@ func (c *commandVolumeCheckDisk) readIndexDatabase(db *needle_map.MemDb, collect
 	if verbose {
 		fmt.Fprintf(writer, "load collection %s volume %d index size %d from %s ...\n", collection, volumeId, buf.Len(), volumeServer)
 	}
-
-	return db.LoadFromReaderAt(bytes.NewReader(buf.Bytes()))
-
+	return db.LoadFilterFromReaderAt(bytes.NewReader(buf.Bytes()), true, false)
 }
 
 func (c *commandVolumeCheckDisk) copyVolumeIndexFile(collection string, volumeId uint32, volumeServer pb.ServerAddress, buf *bytes.Buffer, verbose bool, writer io.Writer) error {
diff --git a/weed/shell/command_volume_fsck.go b/weed/shell/command_volume_fsck.go
index 854929998..6e3a813cf 100644
--- a/weed/shell/command_volume_fsck.go
+++ b/weed/shell/command_volume_fsck.go
@@ -574,7 +574,7 @@ func (c *commandVolumeFsck) oneVolumeFileIdsSubtractFilerFileIds(dataNodeId stri
 		if !n.Size.IsValid() {
 			return nil
 		}
-		orphanFileIds = append(orphanFileIds, fmt.Sprintf("%d,%s00000000", volumeId, n.Key.String()))
+		orphanFileIds = append(orphanFileIds, n.Key.FileId(volumeId))
 		orphanFileCount++
 		orphanDataSize += uint64(n.Size)
 		return nil
diff --git a/weed/storage/needle_map/memdb.go b/weed/storage/needle_map/memdb.go
index f2b161792..d3d47b605 100644
--- a/weed/storage/needle_map/memdb.go
+++ b/weed/storage/needle_map/memdb.go
@@ -145,8 +145,12 @@ func (cm *MemDb) LoadFromIdx(idxName string) (ret error) {
 
 func (cm *MemDb) LoadFromReaderAt(readerAt io.ReaderAt) (ret error) {
 
+	return cm.LoadFilterFromReaderAt(readerAt, true, true)
+}
+
+func (cm *MemDb) LoadFilterFromReaderAt(readerAt io.ReaderAt, isFilterOffsetZero bool, isFilterDeleted bool) (ret error) {
 	return idx.WalkIndexFile(readerAt, 0, func(key NeedleId, offset Offset, size Size) error {
-		if offset.IsZero() || size.IsDeleted() {
+		if (isFilterOffsetZero && offset.IsZero()) || (isFilterDeleted && size.IsDeleted()) {
 			return cm.Delete(key)
 		}
 		return cm.Set(key, offset, size)
diff --git a/weed/storage/types/needle_id_type.go b/weed/storage/types/needle_id_type.go
index e65c862f2..1ea9b0a1a 100644
--- a/weed/storage/types/needle_id_type.go
+++ b/weed/storage/types/needle_id_type.go
@@ -34,6 +34,10 @@ func (k NeedleId) String() string {
 	return strconv.FormatUint(uint64(k), 16)
 }
 
+func (k NeedleId) FileId(volumeId uint32) string {
+	return fmt.Sprintf("%d,%s00000000", volumeId, k.String())
+}
+
 func ParseNeedleId(idString string) (NeedleId, error) {
 	key, err := strconv.ParseUint(idString, 16, 64)
 	if err != nil {