Thanks so much! It works.

One issue that I noticed, however, is that the exporter will still give an
error for an undefined footnote if a footnote is undefined in a heading
that is excluded from export via the exclude tags function. For example if
I have tagged a heading 'noexp' in one of my included files, and list noexp
on the excluded tags line of the header of my master file the exporter will
still complain if there is an undefined footnote under this header.
If I export a master file with this code:
---
#+EXCLUDE_TAGS: noexp archive notes tasks ARCHIVE
#+INCLUDE: "./1WorkingDraft.org"
---
It will complain if there is any undefined footnote reference in
1WorkingDraft.org , regardless if it is under a heading marked with one of
the excluded tags.

It will not complain about this, however, if I explicitly limit the range
of the include function to the headings that I wish to export using a
custom id.
---
#+INCLUDE: "./1WorkingDraft.org::#Chapter1"
---
This problem is not a big issue insofar as it is relatively easy to work
around, and I probably should not have undefined footnote references
hanging around in my org files anyway, but I figure that you should know
about the behaviour, as I do not think that it is intended.

All best,
Leonard

On 6 September 2015 at 21:21, Nicolas Goaziou <mail@nicolasgoaziou.fr>
wrote:

> Hello,
>
> Leonard Randall <leonard.a.randall@gmail.com> writes:
>
> > 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.
> >
>
> [...]
>
> > 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
>
> Fixed. Thank you.
>
> > --- 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]
>
> This is a footnote /definition/ since it starts at column 0.
>
> > * Footnotes
> >
> > [fn:dd1cd1f9] Here is a footnote
>
> This is a second footnote definition for the same label. Syntax is too
> much faulty for a clean export.
>
>
> Regards,
>
> --
> Nicolas Goaziou
>