diff --git a/db/version_builder.cc b/db/version_builder.cc
index e282e670c9..3a4143b9e8 100644
--- a/db/version_builder.cc
+++ b/db/version_builder.cc
@@ -101,22 +101,25 @@ class VersionBuilder::Rep {
     for (int level = 0; level < base_vstorage_->num_levels(); level++) {
       const auto& added = levels_[level].added_files;
       for (auto& pair : added) {
-        FileMetaData* f = pair.second;
-        f->refs--;
-        if (f->refs <= 0) {
-          if (f->table_reader_handle) {
-            assert(table_cache_ != nullptr);
-            table_cache_->ReleaseHandle(f->table_reader_handle);
-            f->table_reader_handle = nullptr;
-          }
-          delete f;
-        }
+        UnrefFile(pair.second);
       }
     }
 
     delete[] levels_;
   }
 
+  void UnrefFile(FileMetaData* f) {
+    f->refs--;
+    if (f->refs <= 0) {
+      if (f->table_reader_handle) {
+        assert(table_cache_ != nullptr);
+        table_cache_->ReleaseHandle(f->table_reader_handle);
+        f->table_reader_handle = nullptr;
+      }
+      delete f;
+    }
+  }
+
   void CheckConsistency(VersionStorageInfo* vstorage) {
 #ifndef NDEBUG
     // make sure the files are sorted correctly
@@ -199,6 +202,12 @@ class VersionBuilder::Rep {
       const auto number = del_file.second;
       levels_[level].deleted_files.insert(number);
       CheckConsistencyForDeletes(edit, number, level);
+
+      auto exising = levels_[level].added_files.find(number);
+      if (exising != levels_[level].added_files.end()) {
+        UnrefFile(exising->second);
+        levels_[level].added_files.erase(number);
+      }
     }
 
     // Add new files
diff --git a/db/version_builder_test.cc b/db/version_builder_test.cc
index 1373e2f88e..5da73cbc33 100644
--- a/db/version_builder_test.cc
+++ b/db/version_builder_test.cc
@@ -126,6 +126,84 @@ TEST(VersionBuilderTest, ApplyAndSaveTo) {
   }
 }
 
+TEST(VersionBuilderTest, ApplyMultipleAndSaveTo) {
+  UpdateVersionStorageInfo();
+
+  VersionEdit version_edit;
+  version_edit.AddFile(2, 666, 0, 100U, GetInternalKey("301"),
+                       GetInternalKey("350"), 200, 200);
+  version_edit.AddFile(2, 676, 0, 100U, GetInternalKey("401"),
+                       GetInternalKey("450"), 200, 200);
+  version_edit.AddFile(2, 636, 0, 100U, GetInternalKey("601"),
+                       GetInternalKey("650"), 200, 200);
+  version_edit.AddFile(2, 616, 0, 100U, GetInternalKey("501"),
+                       GetInternalKey("550"), 200, 200);
+  version_edit.AddFile(2, 606, 0, 100U, GetInternalKey("701"),
+                       GetInternalKey("750"), 200, 200);
+
+  EnvOptions env_options;
+
+  VersionBuilder version_builder(env_options, nullptr, &vstorage_);
+
+  VersionStorageInfo new_vstorage(&icmp_, ucmp_, options_.num_levels,
+                                  kCompactionStyleLevel, nullptr);
+  version_builder.Apply(&version_edit);
+  version_builder.SaveTo(&new_vstorage);
+
+  ASSERT_EQ(500U, new_vstorage.NumLevelBytes(2));
+
+  for (int i = 0; i < new_vstorage.num_levels(); i++) {
+    for (auto* f : new_vstorage.LevelFiles(i)) {
+      if (--f->refs == 0) {
+        delete f;
+      }
+    }
+  }
+}
+
+TEST(VersionBuilderTest, ApplyDeleteAndSaveTo) {
+  UpdateVersionStorageInfo();
+
+  EnvOptions env_options;
+  VersionBuilder version_builder(env_options, nullptr, &vstorage_);
+  VersionStorageInfo new_vstorage(&icmp_, ucmp_, options_.num_levels,
+                                  kCompactionStyleLevel, nullptr);
+
+  VersionEdit version_edit;
+  version_edit.AddFile(2, 666, 0, 100U, GetInternalKey("301"),
+                       GetInternalKey("350"), 200, 200);
+  version_edit.AddFile(2, 676, 0, 100U, GetInternalKey("401"),
+                       GetInternalKey("450"), 200, 200);
+  version_edit.AddFile(2, 636, 0, 100U, GetInternalKey("601"),
+                       GetInternalKey("650"), 200, 200);
+  version_edit.AddFile(2, 616, 0, 100U, GetInternalKey("501"),
+                       GetInternalKey("550"), 200, 200);
+  version_edit.AddFile(2, 606, 0, 100U, GetInternalKey("701"),
+                       GetInternalKey("750"), 200, 200);
+  version_builder.Apply(&version_edit);
+
+  VersionEdit version_edit2;
+  version_edit.AddFile(2, 808, 0, 100U, GetInternalKey("901"),
+                       GetInternalKey("950"), 200, 200);
+  version_edit2.DeleteFile(2, 616);
+  version_edit2.DeleteFile(2, 636);
+  version_edit.AddFile(2, 806, 0, 100U, GetInternalKey("801"),
+                       GetInternalKey("850"), 200, 200);
+  version_builder.Apply(&version_edit2);
+
+  version_builder.SaveTo(&new_vstorage);
+
+  ASSERT_EQ(300U, new_vstorage.NumLevelBytes(2));
+
+  for (int i = 0; i < new_vstorage.num_levels(); i++) {
+    for (auto* f : new_vstorage.LevelFiles(i)) {
+      if (--f->refs == 0) {
+        delete f;
+      }
+    }
+  }
+}
+
 TEST(VersionBuilderTest, EstimatedActiveKeys) {
   const uint32_t kTotalSamples = 20;
   const uint32_t kNumLevels = 5;