diff --git a/src/calibre/devices/kobo/books.py b/src/calibre/devices/kobo/books.py
index 2e3cfca317..29506ddc3f 100644
--- a/src/calibre/devices/kobo/books.py
+++ b/src/calibre/devices/kobo/books.py
@@ -58,6 +58,7 @@ class Book(Book_):
                                 self.datetime = time.gmtime()
 
         self.contentID = None
+        self.current_collections = []
 
         if thumbnail_name is not None:
             self.thumbnail = ImageWrapper(thumbnail_name)
@@ -250,4 +251,3 @@ class KTCollectionsBookList(CollectionsBookList):
 #        debug_print("KTCollectionsBookList:is_debugging - is_debugging=", is_debugging)
 
         return is_debugging
-
diff --git a/src/calibre/devices/kobo/driver.py b/src/calibre/devices/kobo/driver.py
index 8d6e6ad7a4..757093b7a8 100644
--- a/src/calibre/devices/kobo/driver.py
+++ b/src/calibre/devices/kobo/driver.py
@@ -33,11 +33,11 @@ class KOBO(USBMS):
     gui_name = 'Kobo Reader'
     description = _('Communicate with the Kobo Reader')
     author = 'Timothy Legge and David Forrester'
-    version = (2, 0, 1)
+    version = (2, 0, 2)
 
     dbversion = 0
     fwversion = 0
-    supported_dbversion = 62
+    supported_dbversion = 65
     has_kepubs = False
 
     supported_platforms = ['windows', 'osx', 'linux']
@@ -217,7 +217,7 @@ class KOBO(USBMS):
                                 # print 'update_metadata_item returned true'
                                 changed = True
                         else:
-                             debug_print("    Strange:  The file: ", prefix, lpath, " does mot exist!")
+                            debug_print("    Strange:  The file: ", prefix, lpath, " does mot exist!")
                     if lpath in playlist_map and \
                         playlist_map[lpath] not in bl[idx].device_collections:
                             bl[idx].device_collections = playlist_map.get(lpath,[])
@@ -841,6 +841,14 @@ class KOBO(USBMS):
 
 #        debug_print('Finished update_device_database_collections', collections_attributes)
 
+
+    def get_collections_attributes(self):
+        collections = []
+        opts = self.settings()
+        if opts.extra_customization and len(opts.extra_customization[self.OPT_COLLECTIONS]) > 0:
+            collections = [x.lower().strip() for x in opts.extra_customization[self.OPT_COLLECTIONS].split(',')]
+        return collections
+
     def sync_booklists(self, booklists, end_session=True):
 #        debug_print('KOBO: started sync_booklists')
         paths = self.get_device_paths()
@@ -853,12 +861,7 @@ class KOBO(USBMS):
                     blists[i] = booklists[i]
             except IndexError:
                 pass
-        opts = self.settings()
-        if opts.extra_customization:
-            collections = [x.lower().strip() for x in
-                    opts.extra_customization[self.OPT_COLLECTIONS].split(',')]
-        else:
-            collections = []
+        collections = self.get_collections_attributes()
 
         #debug_print('KOBO: collection fields:', collections)
         for i, blist in blists.items():
@@ -1447,6 +1450,7 @@ class KOBOTOUCH(KOBO):
 
                     if lpath in playlist_map:
                         bl[idx].device_collections = playlist_map.get(lpath,[])
+                        bl[idx].current_collections = bl[idx].device_collections
                         changed = True
 
                     if show_debug:
@@ -1483,6 +1487,7 @@ class KOBOTOUCH(KOBO):
 
                     # print 'Update booklist'
                     book.device_collections = playlist_map.get(lpath,[])# if lpath in playlist_map else []
+                    book.current_collections = bl[idx].device_collections
                     book.contentID = ContentID
 #                    debug_print('KoboTouch:update_booklist - title=', title, 'book.device_collections', book.device_collections)
 
@@ -1944,6 +1949,7 @@ class KOBOTOUCH(KOBO):
             if self.supports_bookshelves():
                 debug_print("KoboTouch:update_device_database_collections - managing bookshelves.")
                 if bookshelf_attribute:
+                    debug_print("KoboTouch:update_device_database_collections - bookshelf_attribute=", bookshelf_attribute)
                     for book in booklists:
                         if book.application_id is not None:
 #                            debug_print("KoboTouch:update_device_database_collections - about to remove a book from shelves book.title=%s" % book.title)
@@ -1958,11 +1964,7 @@ class KOBOTOUCH(KOBO):
 
     def rebuild_collections(self, booklist, oncard):
         debug_print("KoboTouch:rebuild_collections")
-        collections_attributes = []
-        opts = self.settings()
-        if opts.extra_customization:
-            collections_attributes = [x.strip() for x in
-                    opts.extra_customization[self.OPT_COLLECTIONS].split(',')]
+        collections_attributes = self.get_collections_attributes()
 
         debug_print('KoboTouch:rebuild_collections: collection fields:', collections_attributes)
         self.update_device_database_collections(booklist, collections_attributes, oncard)
@@ -2086,12 +2088,17 @@ class KOBOTOUCH(KOBO):
 
     def remove_book_from_device_bookshelves(self, connection, book):
         show_debug = self.is_debugging_title(book.title)# or True
+        
+        remove_shelf_list = set(book.current_collections) - set(book.device_collections) - set(["Im_Reading", "Read", "Closed"])
 
         if show_debug:
-            debug_print('KoboTouch:remove_book_from_device_bookshelves - book.in_library="%s"'%book.application_id)
+            debug_print('KoboTouch:remove_book_from_device_bookshelves - book.application_id="%s"'%book.application_id)
             debug_print('KoboTouch:remove_book_from_device_bookshelves - book.contentID="%s"'%book.contentID)
             debug_print('KoboTouch:remove_book_from_device_bookshelves - book.device_collections=', book.device_collections)
-
+            debug_print('KoboTouch:remove_book_from_device_bookshelves - remove_shelf_list=', remove_shelf_list)
+        
+        if len(remove_shelf_list) == 0:
+            return
 
         query = 'DELETE FROM ShelfContent WHERE ContentId = ?'