Hi Nicolas, Thank you for your answer! Nicolas Goaziou writes: >> When a file uses #+include: X.org to structure an org-file and the >> included files use footnotes defined in the master file, export works >> without problems, but sorting the footnotes by reference with >> : C-u M-x org-footnote-action s >> removes the footnotes used in the included files. > 1. test it with the latest Org release (9.2)? I cannot easily test with the latest release, but > 2. and, if that still fails, provide an ECM demonstrating your issue? here’s a minimal release. Add it into an org-file, then create main.org and sub.org with M-x org-babel-tangle. Finally run the code-block in main.org. #+BEGIN_SRC org :tangle main.org ,#+include: sub.org Here is a footnote[fn:1] run the following code block with C-c C-c and answer with =s= ,#+BEGIN_SRC elisp (org-footnote-action t) ,#+END_SRC ,* Footnotes [fn:1] footnote referenced in main [fn:2] footnote referenced in sub #+END_SRC #+BEGIN_SRC org :tangle sub.org This footnote will get lost[fn:2] #+END_SRC Best wishes, Arne -- Unpolitisch sein heißt politisch sein ohne es zu merken