diff --git a/QuestPatcher.Core/Modding/ConfigModProvider.cs b/QuestPatcher.Core/Modding/ConfigModProvider.cs
index b6c1545..6e3e2bb 100644
--- a/QuestPatcher.Core/Modding/ConfigModProvider.cs
+++ b/QuestPatcher.Core/Modding/ConfigModProvider.cs
@@ -13,7 +13,7 @@ public abstract class ConfigModProvider : JsonConverter<IMod>, IModProvider
         public abstract string FileExtension { get; }
         public abstract Task<IMod> LoadFromFile(string modPath);
         public abstract Task DeleteMod(IMod mod);
-        public abstract Task LoadMods();
+        public abstract Task LoadModsStatus();
         public abstract void ClearMods();
         public abstract Task LoadLegacyMods();
     }
diff --git a/QuestPatcher.Core/Modding/IModProvider.cs b/QuestPatcher.Core/Modding/IModProvider.cs
index 9b99777..7882f76 100644
--- a/QuestPatcher.Core/Modding/IModProvider.cs
+++ b/QuestPatcher.Core/Modding/IModProvider.cs
@@ -29,7 +29,7 @@ public interface IModProvider
         /// Loads the mods from the quest.
         /// </summary>
         /// <returns>Task completing when all mods are loaded</returns>
-        Task LoadMods();
+        Task LoadModsStatus();
 
         /// <summary>
         /// Clears currently loaded mods
diff --git a/QuestPatcher.Core/Modding/ModManager.cs b/QuestPatcher.Core/Modding/ModManager.cs
index 7fe3f38..187e34b 100644
--- a/QuestPatcher.Core/Modding/ModManager.cs
+++ b/QuestPatcher.Core/Modding/ModManager.cs
@@ -180,9 +180,15 @@ public async Task LoadModsForCurrentApp()
                 await SaveMods();
             }
 
+            await UpdateModsStatus();
+        }
+
+        public async Task UpdateModsStatus()
+        {
+            Log.Information("Checking if mods are installed");
             foreach (IModProvider provider in _modProviders.Values)
             {
-                await provider.LoadMods();
+                await provider.LoadModsStatus();
             }
         }
 
diff --git a/QuestPatcher.Core/Modding/QModProvider.cs b/QuestPatcher.Core/Modding/QModProvider.cs
index f83c91f..ac3f371 100644
--- a/QuestPatcher.Core/Modding/QModProvider.cs
+++ b/QuestPatcher.Core/Modding/QModProvider.cs
@@ -243,7 +243,7 @@ public override void Write(Utf8JsonWriter writer, IMod value, JsonSerializerOpti
             JsonSerializer.Serialize(writer, AssertQMod(value).Manifest, options);
         }
 
-        public override async Task LoadMods()
+        public override async Task LoadModsStatus()
         {
             List<string> modFiles = await _debugBridge.ListDirectoryFiles(_modManager.ModsPath, true);
             List<string> libFiles = await _debugBridge.ListDirectoryFiles(_modManager.LibsPath, true);
diff --git a/QuestPatcher.Core/Patching/PatchingManager.cs b/QuestPatcher.Core/Patching/PatchingManager.cs
index 621eb91..a76aec0 100644
--- a/QuestPatcher.Core/Patching/PatchingManager.cs
+++ b/QuestPatcher.Core/Patching/PatchingManager.cs
@@ -649,6 +649,8 @@ public async Task PatchApp()
 
             // Recreate the mod directories as they will not be present after the uninstall/backup restore
             await _modManager.CreateModDirectories();
+            // When repatching, certain mods may have been deleted when the app was uninstalled, so we will check for this
+            await _modManager.UpdateModsStatus();
 
             await _installManager.NewApkInstalled(_patchedApkPath);