oops. attached the wrong patch. amended patch follows.

>From b9192f5e9a3bbe9620d9f588313d7f62e33135a5 Mon Sep 17 00:00:00 2001
From: Suhail Shergill <suhailsherg...@gmail.com>
Date: Sun, 8 Apr 2012 10:49:51 -0400
Subject: [PATCH] org-html.el: Make footnotes unique to an entry

* lisp/org-html.el (org-export-as-html): Assign unique ids to footnotes
  if possible

If the entry (or its ancestor) has the CUSTOM_ID property defined, then
use that as part of the generated footnote references and definitions.
---
 lisp/org-html.el |    8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/lisp/org-html.el b/lisp/org-html.el
index c9c9d78..b9123a1 100644
--- a/lisp/org-html.el
+++ b/lisp/org-html.el
@@ -1248,6 +1248,9 @@ PUB-DIR is set, use this as the publishing directory."
 	 (org-export-have-math nil)
 	 (org-export-footnotes-seen nil)
 	 (org-export-footnotes-data (org-footnote-all-labels 'with-defs))
+	 (custom-id (or (org-entry-get nil "CUSTOM_ID" t) ""))
+	 (footnote-def-prefix (format "fn-%s" custom-id))
+	 (footnote-ref-prefix (format "fnr-%s" custom-id))
 	 (lines
 	  (org-split-string
 	   (org-export-preprocess-string
@@ -1685,7 +1688,7 @@ PUB-DIR is set, use this as the publishing directory."
 			  (format
 			   (concat "%s"
 				   (format org-export-html-footnote-format
-					   (concat "<a class=\"footref\" name=\"fnr.%s%s\" href=\"#fn.%s\">%s</a>")))
+					   (concat "<a class=\"footref\" name=\"" footnote-ref-prefix ".%s%s\" href=\"#" footnote-def-prefix ".%s\">%s</a>")))
 			   (or (match-string 1 org-line) "") n extra n n)
 			  ;; If another footnote is following the
 			  ;; current one, add a separator.
@@ -1773,7 +1776,8 @@ PUB-DIR is set, use this as the publishing directory."
 			      (format
 			       (concat "<p class=\"footnote\">"
 				       (format org-export-html-footnote-format
-					       "<a class=\"footnum\" name=\"fn.%s\" href=\"#fnr.%s\">%s</a>"))
+					       (concat
+						"<a class=\"footnum\" name=\"" footnote-def-prefix ".%s\" href=\"#" footnote-ref-prefix ".%s\">%s</a>")))
 			       n n n) t t org-line)))))
 	    ;; Check if the line break needs to be conserved
 	    (cond
-- 
1.7.10


Suhail Shergill <suhailsherg...@gmail.com> writes:

> running org-export-as-html on a subtree is currently problematic if the result
> is to be merged into a document which contains html-ized versions of other
> subtrees: the footnote references and definitions get clobbered.
>
> this patch uses the CUSTOM_ID property of the subtree to generate unique
> footnote references and definitions. if the subtree does not have the 
> CUSTOM_ID
> property set the result is a nop.
>
>
> From 27f89f8bfff334810aba5c33af621e351fa0be79 Mon Sep 17 00:00:00 2001
> From: Suhail Shergill <suhailsherg...@gmail.com>
> Date: Sun, 8 Apr 2012 10:49:51 -0400
> Subject: [PATCH] org-html.el: Make footnotes unique to an entry
>
> * lisp/org-html.el (org-export-as-html): Assign unique ids to footnotes
>   if possible
>
> If the entry (or its ancestor) has the CUSTOM_ID property defined, then
> use that as part of the generated footnote references and definitions.
> ---
>  lisp/org-html.el |   12 ++++++++----
>  1 file changed, 8 insertions(+), 4 deletions(-)
>
> diff --git a/lisp/org-html.el b/lisp/org-html.el
> index c9c9d78..8b79c39 100644
> --- a/lisp/org-html.el
> +++ b/lisp/org-html.el
> @@ -1248,6 +1248,9 @@ PUB-DIR is set, use this as the publishing directory."
>        (org-export-have-math nil)
>        (org-export-footnotes-seen nil)
>        (org-export-footnotes-data (org-footnote-all-labels 'with-defs))
> +      (custom-id (or (org-entry-get nil "CUSTOM_ID" t) ""))
> +      (footnote-def-prefix (format "fn-%s" custom-id))
> +      (footnote-ref-prefix (format "fnr-%s" custom-id))
>        (lines
>         (org-split-string
>          (org-export-preprocess-string
> @@ -1685,8 +1688,8 @@ PUB-DIR is set, use this as the publishing directory."
>                         (format
>                          (concat "%s"
>                                  (format org-export-html-footnote-format
> -                                        (concat "<a class=\"footref\" 
> name=\"fnr.%s%s\" href=\"#fn.%s\">%s</a>")))
> -                        (or (match-string 1 org-line) "") n extra n n)
> +                                        (concat "<a class=\"footref\" 
> name=\"" footnote-ref-prefix ".%s%s\" href=\"#" footnote-def-prefix 
> ".%s\">%s</a>")))
> +                        (or (match-string 1 line) "") n extra n n)
>                         ;; If another footnote is following the
>                         ;; current one, add a separator.
>                         (if (save-match-data
> @@ -1773,8 +1776,9 @@ PUB-DIR is set, use this as the publishing directory."
>                             (format
>                              (concat "<p class=\"footnote\">"
>                                      (format org-export-html-footnote-format
> -                                            "<a class=\"footnum\" 
> name=\"fn.%s\" href=\"#fnr.%s\">%s</a>"))
> -                            n n n) t t org-line)))))
> +                                            (concat
> +                                             "<a class=\"footnum\" name=\"" 
> footnote-def-prefix ".%s\" href=\"#" footnote-ref-prefix ".%s\">%s</a>")))
> +                            n n n) t t line)))))
>           ;; Check if the line break needs to be conserved
>           (cond
>            ((string-match "\\\\\\\\[ \t]*$" org-line)
> -- 
> 1.7.10

-- 
Suhail

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