diff --git a/uSync.BackOffice/SyncHandlers/SyncHandlerBase.cs b/uSync.BackOffice/SyncHandlers/SyncHandlerBase.cs
index ed57382c..c8fe6d54 100644
--- a/uSync.BackOffice/SyncHandlers/SyncHandlerBase.cs
+++ b/uSync.BackOffice/SyncHandlers/SyncHandlerBase.cs
@@ -101,7 +101,10 @@ private int GetCleanParentId(string cleanFile)
             var node = syncFileService.LoadXElement(cleanFile);
             var id = node.Attribute("Id").ValueOrDefault(0);
             if (id != 0) return id;
-            return GetCleanParent(cleanFile)?.Id ?? 0;
+
+            return GetCleanParent(cleanFile)?.Id ?? 
+                (node.GetKey() == Guid.Empty ? -1 : 0);
+
         }
 
         /// <summary>
diff --git a/uSync.BackOffice/SyncHandlers/SyncHandlerRoot.cs b/uSync.BackOffice/SyncHandlers/SyncHandlerRoot.cs
index ac67f358..6a9ec250 100644
--- a/uSync.BackOffice/SyncHandlers/SyncHandlerRoot.cs
+++ b/uSync.BackOffice/SyncHandlers/SyncHandlerRoot.cs
@@ -813,7 +813,7 @@ protected IList<Guid> GetFolderKeys(string folder, bool flat)
                 {
                     var node = XElement.Load(file);
                     var key = node.GetKey();
-                    if (key != Guid.Empty && !keys.Contains(key))
+                    if (!keys.Contains(key))
                     {
                         keys.Add(key);
                     }
@@ -1022,6 +1022,14 @@ public IEnumerable<uSyncAction> Export(Udi udi, string[] folders, HandlerSetting
             if (item != null)
                 return Export(item, folders, settings);
 
+            if (udi.IsRoot && settings.CreateClean)
+            {
+                // for roots we still can create a clean
+                var targetFolder = folders.Last();
+                var filename = Path.Combine(targetFolder, $"{Guid.Empty}.{this.uSyncConfig.Settings.DefaultExtension}");
+                CreateCleanFile(Guid.Empty, filename);
+            }
+
             return uSyncAction.Fail(nameof(udi), this.handlerType, this.ItemType, ChangeType.Fail, $"Item not found {udi}",
                  new KeyNotFoundException(nameof(udi)))
                 .AsEnumerableOfOne();
@@ -1172,7 +1180,7 @@ protected virtual bool HasChildren(TObject item)
         /// </summary>
         protected void CreateCleanFile(Guid key, string filename)
         {
-            if (string.IsNullOrWhiteSpace(filename) || key == Guid.Empty)
+            if (string.IsNullOrWhiteSpace(filename))
                 return;
 
             var folder = Path.GetDirectoryName(filename);