How to remove duplicate messages from Mail in Mavericks (POP)

Hello
I'm having some significant problems with Apple Mail, and despite having researched widely, I haven't been able to find a solution yet. Here is my tale of woe...
My set up is that I use Mail with 5 separate accounts, downloading all messages using POP. I keep all my mail so that I have a permanent record of all conversations, going back more than 10 years - this is about 250,000 emails. I'm running the latest version of Mavericks on a 2010 MBP. I have no intention of moving to IMAP - I need to keep a local archive of all my mail.
A few months ago I was having problems with Mail being very slow to load and search emails. I decided to rebuild the mailboxes, but afterwards discovered that thousands of messages in the inbox of one of my accounts (and some of the sub-folders) had disappeared. Once I realised I tried to go back to a recent Time Machine back up, but, for whatever reason, that part of the back up hadn't worked properly and I was unable to recover the previous status. Ileft it while I decided what to do, and had time to deal with it.
The last 2 years worth of emails on that account were still archived on gmail, so last week I decided to try redownloading the whole lot (something like 72,000 messages), and then uplanned to use one of the scripts I was aware of to remove the duplicates to the trash, and then remove any duplicates in the trash forever. That ought to mean I at least had an archive of the last two years of missing messages, even if I had no record of which ones had been flagged or replied to, etc.
The downloading took about 24 hours to complete, and I now have almost 70,000 messages in the inbox of that account. However, I hadn't figured on two things:
1. Mail 'hides' duplicate messages, meaning that all of the messages I've downloaded are showing as unread, and I can't differentiate the ones I already had in my Inbox, and the new downloads. When I click on those apparently unread messages I can see if they have been replied to or forwarded, etc, but there's no obvious way for me to remove the ones I have already dealt with to the trash, without going through them all manually, which is clearly impossible.
2. The scripts I'd found for removing duplicates don't work. Andreas Amann's Remove Duplicates script doesn't work under Mavericks, and he has abandoned the project. I've also tried the remove-duplicate-messages.scpt made by Jolly Roger (http://jollyroger.kicks-***.org/software/), and while it *sometimes* works on individual subfolders on my Mac (but as far as I can tell removes the duplicate in that folder, rather than the newly downloaded version), mostly it doesn't work at all - it creates a 'Remove Duplicate Messages' folder on my desktop, a log inside it and a folder for removed messages, but nothing appears in the duplicates folder.
So, I'm left in a position where I have 70,000 apparently unread messages in my Inbox, a massively bloated Mail library (which has pretty much doubled in size), a slow and unresponsive Mail program. I figure I have a number of options. Either I could abandon the last week's efforts and revert to the version of

Apologies, this was posted here in error. Please find updated post here: https://discussions.apple.com/message/27261965#27261965

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            qmnum TYPE qmnum,
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            qmnum TYPE qmnum,
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            tplnr TYPE tplnr,
            iloan TYPE iloan,
            END OF ty_iloa,
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            equnr TYPE equnr,
           iloan TYPE iloan,
            ausvn TYPE ausvn,
            ausbs TYPE ausbs,
            auztv TYPE auztv,
            auztb TYPE auztb,
            iwerk TYPE iwerk,
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            indtx TYPE indltx,
            priok TYPE priok,
            strmn TYPE strmn,
            strur TYPE strur,
            ltrmn TYPE ltrmn,
            ltrur TYPE ltrur,
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           arbpl TYPE lgwid,
            vkorg TYPE vkorg,
            vtweg TYPE vtweg,
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            parnr TYPE i_parnr,
            parvw TYPE parvw,
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           objid TYPE cr_objid,
           arbpl1 TYPE arbpl,
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            fecod TYPE fecod,
            fegrp TYPE fegrp,
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            urgrp TYPE urgrp,
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           it_ihpa TYPE STANDARD TABLE OF ty_ihpa,
           it_crhd TYPE STANDARD TABLE OF ty_crhd,
           it_crtx TYPE STANDARD TABLE OF ty_crtx,
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           it_qmur TYPE STANDARD TABLE OF ty_qmur,
           it_iloa TYPE STANDARD TABLE OF ty_iloa,
           it_output TYPE STANDARD TABLE OF ty_output,
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           wa_ihpa TYPE ty_ihpa,
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           wa_crtx TYPE ty_crtx,
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                 wa_crhd,
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              ausvn
              ausbs
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               ltrur
               objnr
               arbpl
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                                                         vkorg
                                                         vtweg
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      CLIENT                        = SY-MANDT
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      HEADER                        =
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      ID                            = 1
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      FILELENGTH                      =
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