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I solved this problem by modifying org/lisp/org-footnote.el Comment out a line in definition of 'org-footnote-re' (defconst org-footnote-re ;; Only [1]-like footnotes are closed in this regexp, as footnotes ;; from other types might contain square brackets (i.e. links) in ;; their definition. ;; ;; `org-re' is used for regexp compatibility with XEmacs. ...

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