diff --git a/nodedb.go b/nodedb.go
index f3aaeea04..1fc4e982d 100644
--- a/nodedb.go
+++ b/nodedb.go
@@ -416,83 +416,42 @@ func (ndb *nodeDB) saveNodeFromPruning(node *Node) error {
 	return ndb.batch.Set(ndb.nodeKey(node.GetKey()), buf.Bytes())
 }
 
-// rootkey cache of two elements, attempting to mimic a direct-mapped cache.
-type rootkeyCache struct {
-	// initial value is set to {-1, -1}, which is an invalid version for a getrootkey call.
-	versions [2]int64
-	rootKeys [2][]byte
-	next     int
-}
-
-func (rkc *rootkeyCache) getRootKey(ndb *nodeDB, version int64) ([]byte, error) {
-	// Check both cache entries
-	for i := 0; i < 2; i++ {
-		if rkc.versions[i] == version {
-			return rkc.rootKeys[i], nil
-		}
-	}
-
-	rootKey, err := ndb.GetRoot(version)
-	if err != nil {
-		return nil, err
-	}
-	rkc.setRootKey(version, rootKey)
-	return rootKey, nil
-}
-
-func (rkc *rootkeyCache) setRootKey(version int64, rootKey []byte) {
-	// Store in next available slot, cycling between 0 and 1
-	rkc.versions[rkc.next] = version
-	rkc.rootKeys[rkc.next] = rootKey
-	rkc.next = (rkc.next + 1) % 2
-}
-
-func newRootkeyCache() *rootkeyCache {
-	return &rootkeyCache{
-		versions: [2]int64{-1, -1},
-		rootKeys: [2][]byte{},
-		next:     0,
-	}
-}
-
 // deleteVersion deletes a tree version from disk.
 // deletes orphans
-func (ndb *nodeDB) deleteVersion(version int64, cache *rootkeyCache) error {
-	rootKey, err := cache.getRootKey(ndb, version)
-	if err != nil && err != ErrVersionDoesNotExist {
+func (ndb *nodeDB) deleteVersion(version int64) error {
+	rootKey, err := ndb.GetRoot(version)
+	if err != nil {
 		return err
 	}
 
 	// If rootKey is nil, it indicates that the root is either a dangling reference or does not exist at all.
 	// In this case, we can skip the orphans pruning process since there are no nodes in the current version to be considered orphans.
 	// Otherwise, proceed with pruning the orphans.
-	if rootKey != nil {
-		if err := ndb.traverseOrphansWithRootkeyCache(cache, version, version+1, func(orphan *Node) error {
-			if orphan.nodeKey.nonce == 0 && !orphan.isLegacy {
-				// if the orphan is a reformatted root, it can be a legacy root
-				// so it should be removed from the pruning process.
-				if err := ndb.deleteFromPruning(ndb.legacyNodeKey(orphan.hash)); err != nil {
-					return err
-				}
-			}
-			if orphan.nodeKey.nonce == 1 && orphan.nodeKey.version < version {
-				// if the orphan is referred to the previous root, it should be reformatted
-				// to (version, 0), because the root (version, 1) should be removed but not
-				// applied now due to the batch writing.
-				orphan.nodeKey.nonce = 0
-			}
-			nk := orphan.GetKey()
-			if orphan.isLegacy {
-				return ndb.deleteFromPruning(ndb.legacyNodeKey(nk))
+	if err := ndb.traverseOrphans(version, version+1, func(orphan *Node) error {
+		if orphan.nodeKey.nonce == 0 && !orphan.isLegacy {
+			// if the orphan is a reformatted root, it can be a legacy root
+			// so it should be removed from the pruning process.
+			if err := ndb.deleteFromPruning(ndb.legacyNodeKey(orphan.hash)); err != nil {
+				return err
 			}
-			return ndb.deleteFromPruning(ndb.nodeKey(nk))
-		}); err != nil && err != ErrVersionDoesNotExist {
-			return err
 		}
+		if orphan.nodeKey.nonce == 1 && orphan.nodeKey.version < version {
+			// if the orphan is referred to the previous root, it should be reformatted
+			// to (version, 0), because the root (version, 1) should be removed but not
+			// applied now due to the batch writing.
+			orphan.nodeKey.nonce = 0
+		}
+		nk := orphan.GetKey()
+		if orphan.isLegacy {
+			return ndb.deleteFromPruning(ndb.legacyNodeKey(nk))
+		}
+		return ndb.deleteFromPruning(ndb.nodeKey(nk))
+	}); err != nil {
+		return err
 	}
 
 	literalRootKey := GetRootKey(version)
-	if rootKey == nil || !bytes.Equal(rootKey, literalRootKey) {
+	if !bytes.Equal(rootKey, literalRootKey) {
 		// if the root key is not matched with the literal root key, it means the given root
 		// is a reference root to the previous version.
 		if err := ndb.deleteFromPruning(ndb.nodeKey(literalRootKey)); err != nil {
@@ -501,7 +460,7 @@ func (ndb *nodeDB) deleteVersion(version int64, cache *rootkeyCache) error {
 	}
 
 	// check if the version is referred by the next version
-	nextRootKey, err := cache.getRootKey(ndb, version+1)
+	nextRootKey, err := ndb.GetRoot(version + 1)
 	if err != nil {
 		return err
 	}
@@ -660,8 +619,8 @@ func (ndb *nodeDB) startPruning() {
 			}
 
 			if err := ndb.deleteVersionsTo(toVersion); err != nil {
-				ndb.logger.Error("Error while pruning", "err", err)
-				time.Sleep(1 * time.Second)
+				ndb.logger.Error("Error while pruning full store asynchronously", "version to prune to", toVersion, "err", err)
+				time.Sleep(500 * time.Millisecond)
 				continue
 			}
 
@@ -731,10 +690,14 @@ func (ndb *nodeDB) deleteVersionsTo(toVersion int64) error {
 		ndb.resetLegacyLatestVersion(-1)
 	}
 
-	rootkeyCache := newRootkeyCache()
 	for version := first; version <= toVersion; version++ {
-		if err := ndb.deleteVersion(version, rootkeyCache); err != nil {
-			return err
+		if err := ndb.deleteVersion(version); err != nil {
+			// If the version is not found in the store continue on to the next version available
+			if err != ErrVersionDoesNotExist {
+				return err
+			}
+
+			ndb.logger.Error("Error while pruning, moving on the the next version in the store", "version missing", version, "next version", version+1, "err", err)
 		}
 		ndb.resetFirstVersion(version + 1)
 	}
@@ -1118,12 +1081,7 @@ func isReferenceRoot(bz []byte) (bool, int) {
 // traverseOrphans traverses orphans which removed by the updates of the curVersion in the prevVersion.
 // NOTE: it is used for both legacy and new nodes.
 func (ndb *nodeDB) traverseOrphans(prevVersion, curVersion int64, fn func(*Node) error) error {
-	cache := newRootkeyCache()
-	return ndb.traverseOrphansWithRootkeyCache(cache, prevVersion, curVersion, fn)
-}
-
-func (ndb *nodeDB) traverseOrphansWithRootkeyCache(cache *rootkeyCache, prevVersion, curVersion int64, fn func(*Node) error) error {
-	curKey, err := cache.getRootKey(ndb, curVersion)
+	curKey, err := ndb.GetRoot(curVersion)
 	if err != nil {
 		return err
 	}
@@ -1133,7 +1091,7 @@ func (ndb *nodeDB) traverseOrphansWithRootkeyCache(cache *rootkeyCache, prevVers
 		return err
 	}
 
-	prevKey, err := cache.getRootKey(ndb, prevVersion)
+	prevKey, err := ndb.GetRoot(prevVersion)
 	if err != nil {
 		return err
 	}