Hi org mode community,

I have my thesis divided into several chapters each with its own org file.
I was trying to use org's Include function to compile a pdf of the complete
draft using a master file. However, I found that if there was more than one
reference to the same footnote in one of my chapter files, the exporter
would complain that a footnote was undefined.

In my case this occurred because I keep old versions of chapter sections
under an archive heading, and at least up til now I did not change the
names of footnotes, when I copied material over from one draft to the next.
It seemed  strange that it would even register these older references,
because I exclude these headlines from export, but it seems to do so. The
problem also occurs if both references are in a headline that is supposed
to be exported.

I am using org version 8.3.1 from elpa, and I am running Emacs 25.0.50.1
compiled for Windows 64. The problem can be reproduced with the following
minimal examples.

Suppose this is the master file:

---- Begin Master.org ---
* Here is my master file
It has an include command.
#+INCLUDE: "./Included.org"
--- End Master.org ---

If I try to export this file it will throw up an error with either one of
the following include files.
--- begin Included.org ---
#+EXCLUDE_TAGS: noexp archive notes
#+ARCHIVE: ::* Archived
* This is a headline.

This is some text. [fn:dd1cd1f9]
* Archive                                                        :archive:
** This is a headline (draft 0)
Here is a previous version of the text to which I affixed the same
footnote. [fn:dd1cd1f9]
* Footnotes

[fn:dd1cd1f9] Here is the footnote

--- end Included.org ---

--- begin Included.org ---
* This is a headline.
This is some text. [fn:dd1cd1f9]

Here is some more text to which I wish to affix the same footnote.
[fn:dd1cd1f9]
* Footnotes

[fn:dd1cd1f9] Here is a footnote

--- end Included.org ---

I get the following backtrace:
---  ---
Debugger entered--Lisp error: (error "Definition not found for footnote
fn:dd1cd1f9 in file c:/Users/leotr/G/P/Tests/Included.org")
  signal(error ("Definition not found for footnote fn:dd1cd1f9 in file
c:/Users/leotr/G/P/Tests/Included.org"))
  error("Definition not found for footnote %s in file %s" "fn:dd1cd1f9"
"c:/Users/leotr/G/P/Tests/Included.org")
  org-export--prepare-file-contents("c:/Users/leotr/G/P/Tests/Included.org"
nil 0 2 1 #s(hash-table size 65 test equal rehash-size 1.5 rehash-threshold
0.8 data ( ...)))
  org-export-expand-include-keyword()
  org-export-as(latex nil nil nil (:output-file "./Main.tex"))
  org-export-to-file(latex "./Main.tex" nil nil nil nil nil)
  org-latex-export-to-latex(nil nil nil nil)
  org-export-dispatch(nil)
  funcall-interactively(org-export-dispatch nil)
  #<subr call-interactively>(org-export-dispatch nil nil)
  ad-Advice-call-interactively(#<subr call-interactively>
org-export-dispatch nil nil)
  apply(ad-Advice-call-interactively #<subr call-interactively>
(org-export-dispatch nil nil))
  call-interactively(org-export-dispatch nil nil)
  command-execute(org-export-dispatch)
---  ---