diff --git a/src/engine/writetransaction.h b/src/engine/writetransaction.h
--- a/src/engine/writetransaction.h
+++ b/src/engine/writetransaction.h
@@ -59,15 +59,18 @@
     void removeRecursively(quint64 parentId, Functor shouldDelete) {
         DocumentUrlDB docUrlDB(m_dbis.idTreeDbi, m_dbis.idFilenameDbi, m_txn);
 
-        if (shouldDelete(parentId)) {
-            removeRecursively(parentId);
+        if (!shouldDelete(parentId)) {
             return;
         }
 
         const QVector<quint64> children = docUrlDB.getChildren(parentId);
         for (quint64 id : children) {
             removeRecursively(id, shouldDelete);
         }
+        // refetch
+        if (docUrlDB.getChildren(parentId).isEmpty()) {
+            removeDocument(parentId);
+        }
     }
 
     void replaceDocument(const Document& doc, DocumentOperations operations);
diff --git a/src/file/indexcleaner.cpp b/src/file/indexcleaner.cpp
--- a/src/file/indexcleaner.cpp
+++ b/src/file/indexcleaner.cpp
@@ -81,7 +81,7 @@
     for (const QString& folder : excludeFolders) {
         quint64 id = filePathToId(QFile::encodeName(folder));
         if (tr.hasDocument(id)) {
-            tr.removeRecursively(id);
+            tr.removeRecursively(id, shouldDelete);
         }
     }
     tr.commit();