diff --git a/ModpackUpdater/AppConfig.vb b/ModpackUpdater/AppConfig.vb
index 7ec90b5..213865f 100644
--- a/ModpackUpdater/AppConfig.vb
+++ b/ModpackUpdater/AppConfig.vb
@@ -9,10 +9,12 @@ Public Class AppConfig
     Public Property LastConfigFilePath As String
     Public Property KeepLocalFiles As New List(Of String)
     Public Property RemoveLocalFiles As Boolean
+    Public Property OnlySearchSubfolders As Boolean
 
     Public Sub Reset()
         KeepLocalFiles.Clear()
         KeepLocalFiles.Add("OptiFine_1.7.10_HD_U_E7.jar")
+        OnlySearchSubfolders = True
     End Sub
 
     Public Shared ReadOnly Property Instance As AppConfig
diff --git a/ModpackUpdater/ModpackUpdater.vbproj b/ModpackUpdater/ModpackUpdater.vbproj
index 4007614..c248635 100644
--- a/ModpackUpdater/ModpackUpdater.vbproj
+++ b/ModpackUpdater/ModpackUpdater.vbproj
@@ -8,7 +8,7 @@
     <ApplicationIcon>icons8_download_from_ftp.ico</ApplicationIcon>
     <AssemblyName>Minecraft Modpack Updater</AssemblyName>
     <IncludeAllContentForSelfExtract>true</IncludeAllContentForSelfExtract>
-    <Version>1.2.1.0</Version>
+    <Version>1.2.2.0</Version>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|AnyCPU'">
     <DebugSymbols>true</DebugSymbols>
diff --git a/ModpackUpdater/UpdateInstaller.vb b/ModpackUpdater/UpdateInstaller.vb
index 74d57da..fe0c557 100644
--- a/ModpackUpdater/UpdateInstaller.vb
+++ b/ModpackUpdater/UpdateInstaller.vb
@@ -89,6 +89,7 @@ Public Class UpdateInstaller
             Dim allLocalFiles = Directory.GetFiles(localPath, "*", SearchOption.AllDirectories)
             For Each lf As String In allLocalFiles
                 Dim isKnown As Boolean = False
+                Dim allowRemove As Boolean = AppConfig.Instance.OnlySearchSubfolders OrElse Path.GetDirectoryName(lf) <> localPath
 
                 For Each checkedFile As String In checkedFiles
                     If Not isKnown AndAlso If(checkedFile, "") = If(lf, "") Then
@@ -96,7 +97,7 @@ Public Class UpdateInstaller
                     End If
                 Next
 
-                If Not isKnown Then
+                If Not isKnown AndAlso allowRemove Then
                     result.SyncFiles.Add(New UpdateSyncFile(If(ignoreRevmoedFiles, UpdateSyncAction.None, UpdateSyncAction.RemovedFile), lf, String.Empty))
                 End If
             Next