Index: builder.py
===================================================================
--- builder.py	(revision 58006)
+++ builder.py	(working copy)
@@ -498,7 +498,7 @@
         except (IOError, OSError):
             pass
         # delete all entries for files that will be rebuilt
-        self.indexer.prune(set(self.env.all_files) - set(filenames))
+        self.indexer.prune([fn[:-4] for fn in set(self.env.all_files) - set(filenames)])
 
     def index_file(self, filename, doctree, title):
         # only index pages with title