diff --git a/src/calibre/ebooks/conversion/plugins/epub_input.py b/src/calibre/ebooks/conversion/plugins/epub_input.py
index e19d466659..bb60412e1b 100644
--- a/src/calibre/ebooks/conversion/plugins/epub_input.py
+++ b/src/calibre/ebooks/conversion/plugins/epub_input.py
@@ -211,8 +211,7 @@ class EPUBInput(InputFormatPlugin):
                     cover_toc_item = item
                     break
             spine = {x.href for x in oeb.spine}
-            if (cover_toc_item is not None and cover_toc_item.count() == 0 and
-                    cover_toc_item not in spine):
+            if (cover_toc_item is not None and cover_toc_item not in spine):
                 oeb.toc.item_that_refers_to_cover = cover_toc_item
 
 
diff --git a/src/calibre/ebooks/conversion/plumber.py b/src/calibre/ebooks/conversion/plumber.py
index 8d523f431a..615ea521d8 100644
--- a/src/calibre/ebooks/conversion/plumber.py
+++ b/src/calibre/ebooks/conversion/plumber.py
@@ -1015,7 +1015,7 @@ OptionRecommendation(name='search_replace',
             # Remove the toc reference to the html cover, if any, except for
             # epub, as the epub output plugin will do the right thing with it.
             item = getattr(self.oeb.toc, 'item_that_refers_to_cover', None)
-            if item is not None:
+            if item is not None and item.count() == 0:
                 self.oeb.toc.remove(item)
 
         from calibre.ebooks.oeb.transforms.flatcss import CSSFlattener