diff --git a/Bloxstrap/Bootstrapper.cs b/Bloxstrap/Bootstrapper.cs
index 0319397..f2330f6 100644
--- a/Bloxstrap/Bootstrapper.cs
+++ b/Bloxstrap/Bootstrapper.cs
@@ -1259,8 +1259,17 @@ namespace Bloxstrap
                 }
             }
 
-            App.RobloxState.Prop.ModManifest = modFolderFiles;
-            App.RobloxState.Save();
+            // make sure we're not overwriting a new update
+            // if we're the background update process, always overwrite
+            if (App.LaunchSettings.BackgroundUpdaterFlag.Active || !App.RobloxState.HasFileOnDiskChanged())
+            {
+                App.RobloxState.Prop.ModManifest = modFolderFiles;
+                App.RobloxState.Save();
+            }
+            else
+            {
+                App.Logger.WriteLine(LOG_IDENT, "RobloxState disk mismatch, not saving ModManifest");
+            }
 
             App.Logger.WriteLine(LOG_IDENT, $"Finished checking file mods");
 
diff --git a/Bloxstrap/JsonManager.cs b/Bloxstrap/JsonManager.cs
index bb1eb77..6c04a2a 100644
--- a/Bloxstrap/JsonManager.cs
+++ b/Bloxstrap/JsonManager.cs
@@ -8,6 +8,11 @@ namespace Bloxstrap
         
         public T Prop { get; set; } = new();
 
+        /// <summary>
+        /// The file hash when last retrieved from disk
+        /// </summary>
+        public string? LastFileHash { get; private set; }
+
         public virtual string ClassName => typeof(T).Name;
 
         public virtual string FileLocation => Path.Combine(Paths.Base, $"{ClassName}.json");
@@ -22,12 +27,15 @@ namespace Bloxstrap
 
             try
             {
-                T? settings = JsonSerializer.Deserialize<T>(File.ReadAllText(FileLocation));
+                string contents = File.ReadAllText(FileLocation);
+
+                T? settings = JsonSerializer.Deserialize<T>(contents);
 
                 if (settings is null)
                     throw new ArgumentNullException("Deserialization returned null");
 
                 Prop = settings;
+                LastFileHash = MD5Hash.FromString(contents);
 
                 App.Logger.WriteLine(LOG_IDENT, "Loaded successfully!");
             }
@@ -74,7 +82,11 @@ namespace Bloxstrap
 
             try
             {
-                File.WriteAllText(FileLocation, JsonSerializer.Serialize(Prop, new JsonSerializerOptions { WriteIndented = true }));
+                string contents = JsonSerializer.Serialize(Prop, new JsonSerializerOptions { WriteIndented = true });
+
+                File.WriteAllText(FileLocation, contents);
+
+                LastFileHash = MD5Hash.FromString(contents);
             }
             catch (Exception ex) when (ex is IOException or UnauthorizedAccessException)
             {
@@ -89,5 +101,13 @@ namespace Bloxstrap
 
             App.Logger.WriteLine(LOG_IDENT, "Save complete!");
         }
+
+        /// <summary>
+        /// Is the file on disk different to the one deserialised during this session?
+        /// </summary>
+        public bool HasFileOnDiskChanged()
+        {
+            return LastFileHash != MD5Hash.FromFile(FileLocation);
+        }
     }
 }
diff --git a/Bloxstrap/Utility/MD5Hash.cs b/Bloxstrap/Utility/MD5Hash.cs
index c282c0a..df49d44 100644
--- a/Bloxstrap/Utility/MD5Hash.cs
+++ b/Bloxstrap/Utility/MD5Hash.cs
@@ -25,6 +25,11 @@ namespace Bloxstrap.Utility
             return FromStream(stream);
         }
 
+        public static string FromString(string str)
+        {
+            return FromBytes(Encoding.UTF8.GetBytes(str));
+        }
+
         public static string Stringify(byte[] hash)
         {
             return BitConverter.ToString(hash).Replace("-", "").ToLowerInvariant();