Fix inventory item ID mapping, PokedexLA save, SuperTrain bags

- Inventory: use model.Index for write-back instead of Array.IndexOf
  by name (118+ duplicate English item names caused silent corruption)
- InventoryItemModel: sync Index when ItemName changes via combo box
- PokedexLA: Save() now writes Seen/ResearchLevel/Perfect back to dex
  (was silently discarding all user edits)
- PokedexSave8a: expose SetPokeHasBeenUpdatedFlag, SetPokeResearchRate,
  SetPokePerfect write methods for ViewModel use
- SuperTrain6: clear trailing bag slots after compaction to prevent
  stale ghost bags (format has no count field)

PKHeX.Avalonia/ViewModels/Subforms/BatchEditorViewModel.cs

@@ -39,8 +39,13 @@ public partial class BatchEditorViewModel : SaveEditorViewModelBase
     /// </summary>
     public int CurrentBox { get; set; }
 
+    private readonly SaveFile _origin;
+    private readonly SaveFile _sav;
+
     public BatchEditorViewModel(SaveFile sav) : base(sav)
     {
+        _origin = sav;
+        _sav = (SaveFile)sav.Clone();
     }
 
     [RelayCommand]
@@ -79,6 +84,7 @@ private async Task ExecuteAsync()
         try
         {
             var result = await Task.Run(() => RunBatchEdit(sets));
+            _origin.CopyChangesFrom(_sav);
             ResultLog = result;
             Modified = true;
         }
@@ -107,15 +113,15 @@ private string RunBatchEdit(StringInstructionSet[] sets)
         switch (SelectedScope)
         {
             case 0: // Current Box
-                SlotInfoLoader.AddBoxData(SAV, data);
+                SlotInfoLoader.AddBoxData(_sav, data);
                 // Filter to current box only
                 data = data.Where(s => s.Source is SlotInfoBox b && b.Box == CurrentBox).ToList();
                 break;
             case 1: // All Boxes
-                SlotInfoLoader.AddBoxData(SAV, data);
+                SlotInfoLoader.AddBoxData(_sav, data);
                 break;
             case 2: // Party
-                SlotInfoLoader.AddPartyData(SAV, data);
+                SlotInfoLoader.AddPartyData(_sav, data);
                 break;
         }
 
@@ -133,9 +139,9 @@ private string RunBatchEdit(StringInstructionSet[] sets)
             }
         }
 
-        // Write back modified data
+        // Write back modified data to clone
         foreach (var slot in data)
-            slot.Source.WriteTo(SAV, slot.Entity, EntityImportSettings.None);
+            slot.Source.WriteTo(_sav, slot.Entity, EntityImportSettings.None);
 
         return editor.GetEditorResults(sets);
     }

PKHeX.Avalonia/ViewModels/Subforms/InventoryItemModel.cs

@@ -1,3 +1,4 @@
+using System;
 using System.Collections.Generic;
 using CommunityToolkit.Mvvm.ComponentModel;
 using PKHeX.Core;
@@ -10,6 +11,8 @@ namespace PKHeX.Avalonia.ViewModels.Subforms;
 /// </summary>
 public partial class InventoryItemModel : ObservableObject
 {
+    private readonly string[] _itemNames;
+
     [ObservableProperty]
     private string _itemName;
 
@@ -33,8 +36,18 @@ public InventoryItemModel(InventoryItem item, string[] itemNames, IReadOnlyList<
     {
         BackingItem = item;
         ValidItems = validItems;
+        _itemNames = itemNames;
         _index = item.Index;
         _count = item.Count;
         _itemName = item.Index < itemNames.Length ? itemNames[item.Index] : $"(Item #{item.Index:000})";
     }
+
+    partial void OnItemNameChanged(string value)
+    {
+        // Update Index when the user changes the item name (e.g. via text edit).
+        // This keeps Index in sync so WriteBackAllPouches can use it directly.
+        var id = Array.IndexOf(_itemNames, value);
+        if (id >= 0)
+            Index = id;
+    }
 }

PKHeX.Avalonia/ViewModels/Subforms/InventoryViewModel.cs

@@ -113,10 +113,7 @@ private void WriteBackAllPouches()
 
             foreach (var itemModel in pouchModel.Items)
             {
-                var itemName = itemModel.ItemName;
-                var itemId = Array.IndexOf(_itemNames, itemName);
-                if (itemId < 0)
-                    itemId = 0;
+                var itemId = itemModel.Index;
 
                 var count = itemModel.Count;
 

PKHeX.Avalonia/ViewModels/Subforms/PokedexLAViewModel.cs

@@ -110,6 +110,15 @@ private void ApplyFilter()
     [RelayCommand]
     private void Save()
     {
+        // Write edited entry values back to the dex data before copying.
+        foreach (var entry in AllEntries)
+        {
+            var species = entry.Species;
+            _dex.SetPokeHasBeenUpdatedFlag(species, entry.Seen);
+            _dex.SetPokeResearchRate(species, entry.ResearchLevel);
+            _dex.SetPokePerfect(species, entry.Perfect);
+        }
+
         _origin.CopyChangesFrom(_sav);
         Modified = true;
     }

PKHeX.Avalonia/ViewModels/Subforms/SAVSuperTrain6ViewModel.cs

@@ -143,7 +143,7 @@ private void Save()
     {
         SaveStageRecord(SelectedStageIndex);
 
-        // Save bags
+        // Save bags (compact non-empty slots to the front)
         int emptySlots = 0;
         for (int i = 0; i < 12; i++)
         {
@@ -156,6 +156,10 @@ private void Save()
             _stb.SetBag(i - emptySlots, (byte)bagIndex);
         }
 
+        // Clear trailing stale slots left after compaction
+        for (int i = 12 - emptySlots; i < 12; i++)
+            _stb.SetBag(i, 0);
+
         _origin.CopyChangesFrom(_sav);
         Modified = true;
     }

PKHeX.Core/Saves/Substructures/Gen8/LA/Pokedex/PokedexSave8a.cs

@@ -138,6 +138,27 @@ public int GetPokeResearchRate(ushort species)
 
     public bool IsPerfect(ushort species) => SaveData.IsPerfect(species);
 
+    public void SetPokeHasBeenUpdatedFlag(ushort species, bool value)
+    {
+        if (species >= MAX_SPECIES)
+            return;
+        SaveData.GetResearchEntry(species).HasEverBeenUpdated = value;
+    }
+
+    public void SetPokeResearchRate(ushort species, int value)
+    {
+        if (species >= MAX_SPECIES)
+            return;
+        SaveData.GetResearchEntry(species).ResearchRate = (ushort)Math.Min(Math.Max(value, 0), PokedexConstants8a.MaxPokedexResearchPoints);
+    }
+
+    public void SetPokePerfect(ushort species, bool value)
+    {
+        if (species >= MAX_SPECIES)
+            return;
+        SaveData.GetResearchEntry(species).IsPerfect = value;
+    }
+
     public int GetUpdateIndex(ushort species) => SaveData.GetResearchEntry(species).UpdateCounter;
     public int GetLastReportedIndex(ushort species) => SaveData.GetResearchEntry(species).LastUpdatedReportCounter;