If you're really missing files from SAGE_ROOT/devel/sage/doc/en/reference, then you could just manually copy them from an old installation of Sage (maybe just copy over the whole directory), or copy them from the main Sage spkg (sage-4.6.2.....spkg), or you could revert those files from a previous version of your Mercurial repository. As Volker said, you should perhaps try deleting the directory .../sage/doc/output.
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