diff --git a/SabreTools.DatFiles/ItemDictionaryDB.cs b/SabreTools.DatFiles/ItemDictionaryDB.cs
index 49c35528..12ef53c1 100644
--- a/SabreTools.DatFiles/ItemDictionaryDB.cs
+++ b/SabreTools.DatFiles/ItemDictionaryDB.cs
@@ -231,6 +231,36 @@ namespace SabreTools.DatFiles
             return _machineIndex - 1;
         }
 
+        /// <summary>
+        /// Remove any keys that have null or empty values
+        /// </summary>
+        public void ClearEmpty()
+        {
+            var keys = SortedKeys.Where(k => k != null).ToList();
+            foreach (string key in keys)
+            {
+                // If the key doesn't exist, skip
+                if (!_buckets.ContainsKey(key))
+                    continue;
+
+                // If the value is null, remove
+                else if (_buckets[key] == null)
+#if NET40_OR_GREATER || NETCOREAPP
+                    _buckets.TryRemove(key, out _);
+#else
+                    _buckets.Remove(key);
+#endif
+
+                // If there are no non-blank items, remove
+                else if (!_buckets[key]!.Any(i => GetItem(i) != null && GetItem(i) is not Blank))
+#if NET40_OR_GREATER || NETCOREAPP
+                    _buckets.TryRemove(key, out _);
+#else
+                    _buckets.Remove(key);
+#endif
+            }
+        }
+
         /// <summary>
         /// Remove all items marked for removal
         /// </summary>
diff --git a/SabreTools.DatTools/Verification.cs b/SabreTools.DatTools/Verification.cs
index 9fa0762f..18124561 100644
--- a/SabreTools.DatTools/Verification.cs
+++ b/SabreTools.DatTools/Verification.cs
@@ -108,6 +108,7 @@ namespace SabreTools.DatTools
             datFile.Header.SetFieldValue<string?>(Models.Metadata.Header.NameKey, $"fixDAT_{datFile.Header.GetStringFieldValue(Models.Metadata.Header.NameKey)}");
             datFile.Header.SetFieldValue<string?>(Models.Metadata.Header.DescriptionKey, $"fixDAT_{datFile.Header.GetStringFieldValue(Models.Metadata.Header.DescriptionKey)}");
             datFile.Items.ClearMarked();
+            datFile.ItemsDB.ClearMarked();
 
             return success;
         }
@@ -157,6 +158,7 @@ namespace SabreTools.DatTools
             datFile.Header.SetFieldValue<string?>(Models.Metadata.Header.NameKey, $"fixDAT_{datFile.Header.GetStringFieldValue(Models.Metadata.Header.NameKey)}");
             datFile.Header.SetFieldValue<string?>(Models.Metadata.Header.DescriptionKey, $"fixDAT_{datFile.Header.GetStringFieldValue(Models.Metadata.Header.DescriptionKey)}");
             datFile.Items.ClearMarked();
+            datFile.ItemsDB.ClearMarked();
 
             return success;
         }
diff --git a/SabreTools.Filtering/Cleaner.cs b/SabreTools.Filtering/Cleaner.cs
index b059394e..cfe1ea6c 100644
--- a/SabreTools.Filtering/Cleaner.cs
+++ b/SabreTools.Filtering/Cleaner.cs
@@ -139,10 +139,14 @@ namespace SabreTools.Filtering
 
                 // Remove all marked items
                 datFile.Items.ClearMarked();
+                datFile.ItemsDB.ClearMarked();
 
                 // We remove any blanks, if we aren't supposed to have any
                 if (KeepEmptyGames == false)
+                {
                     datFile.Items.ClearEmpty();
+                    datFile.ItemsDB.ClearEmpty();
+                }
             }
             catch (Exception ex) when (!throwOnError)
             {
diff --git a/SabreTools/Features/Batch.cs b/SabreTools/Features/Batch.cs
index fc164b32..897728cd 100644
--- a/SabreTools/Features/Batch.cs
+++ b/SabreTools/Features/Batch.cs
@@ -431,7 +431,9 @@ Reset the internal state:           reset();";
                 // Cleanup after the filter
                 // TODO: We might not want to remove immediately
                 batchState.DatFile.Items.ClearMarked();
+                batchState.DatFile.ItemsDB.ClearMarked();
                 batchState.DatFile.Items.ClearEmpty();
+                batchState.DatFile.ItemsDB.ClearEmpty();
             }
         }
 
diff --git a/SabreTools/Features/Sort.cs b/SabreTools/Features/Sort.cs
index 4b36b646..3e1b5be5 100644
--- a/SabreTools/Features/Sort.cs
+++ b/SabreTools/Features/Sort.cs
@@ -119,6 +119,7 @@ namespace SabreTools.Features
                         datdata.Header.SetFieldValue<string?>(Models.Metadata.Header.NameKey, $"fixDAT_{Header.GetStringFieldValue(Models.Metadata.Header.NameKey)}");
                         datdata.Header.SetFieldValue<string?>(Models.Metadata.Header.DescriptionKey, $"fixDAT_{Header.GetStringFieldValue(Models.Metadata.Header.DescriptionKey)}");
                         datdata.Items.ClearMarked();
+                        datdata.ItemsDB.ClearMarked();
                         Writer.Write(datdata, OutputDir);
                     }
                 }
@@ -160,6 +161,7 @@ namespace SabreTools.Features
                     datdata.Header.SetFieldValue<string?>(Models.Metadata.Header.NameKey, $"fixDAT_{Header.GetStringFieldValue(Models.Metadata.Header.NameKey)}");
                     datdata.Header.SetFieldValue<string?>(Models.Metadata.Header.DescriptionKey, $"fixDAT_{Header.GetStringFieldValue(Models.Metadata.Header.DescriptionKey)}");
                     datdata.Items.ClearMarked();
+                    datdata.ItemsDB.ClearMarked();
                     Writer.Write(datdata, OutputDir);
                 }
             }