From mboxrd@z Thu Jan  1 00:00:00 1970
From: Jambunathan K <kjambunathan@gmail.com>
Subject: Re: org-html: subtree specific footnote references
Date: Tue, 10 Jul 2012 11:24:48 +0530
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To: Suhail Shergill <suhailshergill@gmail.com>
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Suhail Shergill <suhailshergill@gmail.com> writes:

> i'm talking about a scenario where for one reason or another you may
> not want to do that, but may instead only want to export the most
> recent subtree which has been added (since the last time it was
> exported).

You are trying to merge two /instances of export command/ and not two
/instances of subtrees/.  It only so happens that, in your specific
case, you are selecting different subtrees for different export
instances.

What is the value of `org-footnote-section' in your case?

Wrt footnotes, what you see in the Org file is not what the exporter
sees.  Footnote definitions get collected in to the buffer at a suitable
point as part of pre-processing (see `org-footnote-normalize').  Also
footnote definitions can be placed by hand at arbitrary points through
out your Org file.

I have a feeling that patch requires more additions.  Furthermore, you
also need to submit a patch to org-e-html.el which will replace
org-html.el in the future.

I will let the owners of org-html.el to take over from here.