diff --git a/osu.Game/Beatmaps/BeatmapStore.cs b/osu.Game/Beatmaps/BeatmapStore.cs
index d1c33d1151..97cfdcf31b 100644
--- a/osu.Game/Beatmaps/BeatmapStore.cs
+++ b/osu.Game/Beatmaps/BeatmapStore.cs
@@ -21,7 +21,7 @@ namespace osu.Game.Beatmaps
         /// The current version of this store. Used for migrations (see <see cref="PerformMigration(int, int)"/>).
         /// The initial version is 1.
         /// </summary>
-        protected override int StoreVersion => 1;
+        protected override int StoreVersion => 2;
 
         public BeatmapStore(SQLiteConnection connection)
             : base(connection)
@@ -74,14 +74,9 @@ namespace osu.Game.Beatmaps
                 switch (currentVersion)
                 {
                     case 1:
-                        // initialising from a version before we had versioning (or a fresh install).
-
-                        // force adding of Protected column (not automatically migrated).
-                        Connection.MigrateTable<BeatmapSetInfo>();
-
-                        // remove all existing beatmaps.
-                        foreach (var b in Connection.GetAllWithChildren<BeatmapSetInfo>(null, true))
-                            Connection.Delete(b, true);
+                    case 2:
+                        // cannot migrate; breaking underlying changes.
+                        Reset();
                         break;
                 }
             }
diff --git a/osu.Game/IO/FileStore.cs b/osu.Game/IO/FileStore.cs
index e35382ea8c..94c9697922 100644
--- a/osu.Game/IO/FileStore.cs
+++ b/osu.Game/IO/FileStore.cs
@@ -23,6 +23,8 @@ namespace osu.Game.IO
 
         public readonly ResourceStore<byte[]> Store;
 
+        protected override int StoreVersion => 2;
+
         public FileStore(SQLiteConnection connection, Storage storage) : base(connection, storage)
         {
             Store = new NamespacedResourceStore<byte[]>(new StorageBackedResourceStore(storage), prefix);
@@ -35,7 +37,19 @@ namespace osu.Game.IO
         protected override void Prepare(bool reset = false)
         {
             if (reset)
+            {
+                try
+                {
+                    foreach (var f in Query<FileInfo>())
+                        Storage.Delete(Path.Combine(prefix, f.Hash));
+                }
+                catch
+                {
+                    // we don't want to ever crash as a result of a reset operation.
+                }
+
                 Connection.DropTable<FileInfo>();
+            }
 
             Connection.CreateTable<FileInfo>();
         }
@@ -46,6 +60,28 @@ namespace osu.Game.IO
             deletePending();
         }
 
+        /// <summary>
+        /// Perform migrations between two store versions.
+        /// </summary>
+        /// <param name="currentVersion">The current store version. This will be zero on a fresh database initialisation.</param>
+        /// <param name="targetVersion">The target version which we are migrating to (equal to the current <see cref="StoreVersion"/>).</param>
+        protected override void PerformMigration(int currentVersion, int targetVersion)
+        {
+            base.PerformMigration(currentVersion, targetVersion);
+
+            while (currentVersion++ < targetVersion)
+            {
+                switch (currentVersion)
+                {
+                    case 1:
+                    case 2:
+                        // cannot migrate; breaking underlying changes.
+                        Reset();
+                        break;
+                }
+            }
+        }
+
         public FileInfo Add(Stream data)
         {
             string hash = data.ComputeSHA2Hash();