diff --git a/src/calibre/devices/kobo/driver.py b/src/calibre/devices/kobo/driver.py
index 907a8b309a..2ef2c5efb7 100644
--- a/src/calibre/devices/kobo/driver.py
+++ b/src/calibre/devices/kobo/driver.py
@@ -2490,7 +2490,8 @@ class KOBOTOUCH(KOBO):
                                  "WHERE Type = 'Shelf' "
                                  "AND NOT EXISTS "
                                     "(SELECT 1 FROM Shelf "
-                                    "WHERE Shelf.Name = Activity.Id)"
+                                    "WHERE Shelf.Name = Activity.Id "
+                                    "AND Shelf._IsDeleted = 'false')"
                                  )
 
         cursor = connection.cursor()