Tidying Apple Mail-at my wits end...

Question

I've literally been battling this scenario, on and off, for well over a week now, probably closer to two weeks. All I'm trying to do is save, then delete some emails. But I just cant seem to get it done. Here are some details...
At work, we're using Apple Mail as the front end to a Gmail Account. They're connected via IMAP. A couple of weeks ago, the boss man said his HD was nearly full and Mail was the main suspect. Yeah, I'll say! A 200GB Mail folder is a little excessive. So I decided that I would spear-head the clean-up efforts. We're a photography business. We send / receive a lot of emails and we have a ton of massive attachments all the time. The whole email "system", which pre-dates my involvement with the company, is so convoluted it's scary. I don't even know how many emails we're talking about. We'll over 40,000.
Here's my general tactic so far. I made a Smart Mailbox to show me everything from 2011, including Sent but not including Trash. This was to be my main filter. I made another Smart Mailbox, identical to this one, but I also had it reveal emails that specifically "Contain Attachments". I went into this Smart Mailbox and tried to select all and chose to Remove Attacments. This would eventually lock Mail up, I'd have to force quit and try again. I eventually sorted this on Size and started at the top and would select small clusters of emails and remove attachments. I did this long enough and often enough to eventually remove all the attachments. Although this is where an anomaly revealed itself. When I would bounce back over to the "all 2011" Smart Mailbox, some of those emails seemed to have attachments still. Huh? A lot of them still had attachments. I thought I'd just dumped these attachments? So I did another Select All, in the full 2011 Smart Mailbox and selected Remove attachments. This too choked things down to the point of needing to force quit Mail. Upon re-launching, one of the many times I needed to, Mail acted almost like it had been initialized and needed to be set up again. Not from scratch, but it did want to re-import 35K emails. I waited this out and eventually it seemed to come back to life. Although this is where Anomaly #2 came in. The IMAP account seemed okay. But I also have my own work email in Apple Mail too, a POP account. Instead of the 1,500 emails I should have had in my own inbox, there were essentially none. No drafts (should've been a dozen.) No Sents and about 6, very recent, emails in my inbox. So my account got toasted along the way! Great. This was days ago. I'm delirious from struggling this with for so long...
After nearly pulling all my hair out, I was finally able to archive all of 2011. The general process was to
1.) Make 2011 Smart Mailbox
2.) Remove Attachments
3.) Save as: Raw Message Source
4.) Delete 2011 emails
This took our 200GB Mail folder down to around 60GB. Hooray! Though, now it was (is) time to try the same move with 2012.
I tried the exact procedure and found pretty much the same oddities: despite having "removed attachments" for the 2012-with-Attachments Smart Mailbox, when I'd move to the "Everything 2012" Smart Mailbox, there were still (large) attachments floating around inside. Again: huh? This stil does not make sense to me, but a some point I had already given up trying to make sense of a lot of this. But I did the same thing: stayed inside 2012 Everything and tried removing more attachments. I've been doing this crap for another week now as once Mail got relaunched, emails with supposedly removed attachments, were re-appearing with their attachments attached. Stil scratching my head on that one...
So now I'm at the point where I'm over it! I'm done trying to remove attachments. I'm simply trying to do a Save As, Raw Message Source, like before. I don't care how large the resulting mbox file may be. But the issue now is a ridiculous amount of waiting—again. When I reveal the Activity Window I'm seeing long, long waits in a few areas: "updating cache directory" and "fetching headers" to name a few. I'm trying the "Save As" right now, as I type and I'd say in the past hour, the status bar *may* have move .1 %—if that!!
What can I do? Do I just need to wait, what feels like is going to be a year, for this process to complete? What about my, essentially lost, emails. (When I log into gmail, via the web, I can see the emails "labeled" with MY address are still there. At least 1,000 of them.)
I can't express how frustrating this has become. I'm a photo editor. I'm supposed to be editing. But I'm technically savvy and have been using Macs for over a decade so these kinds of tasks also, by default, fall into my jurisdiction. I'm *just* trying to archive some emails. I had no idea it would take TWO SOLID weeks. And. I'm not even done. I'd be different if I spent two weeks to get it completed. I've spent two weeks and I'm not even half way done.
I'm feeling so defeated.
Any words of wisdom or guidance at this point would be greatly appreciated. I can provide any kind of additional info that may be needed. The system that I'm trying this on is an iMac running 10.6.8. The bosses machine with the clogged HD is a white plastic MacBook running 10.6.8. He also has this IMAP/Gmail account up and running on our Mac Mini running 10.8.3. FWIW, my POP account is not installed on these latter two machines. I just took a look at the Mail folder on the Mini and it's at about 53GB. What can I do to get out of this straight jacket. What sort of tactics should I be employing, more regularly, to not end up in this torture room that I'm sitting in now...
Thanks for listening!
That top bar, Saving 39027 messages, hasn't budged at all. It's been running for over an hour now...
The one beneath has only moved as far as shown, in the same time—over an hour. Ugh.

Answer 1

Hopefully, it's working. Slow and steady. [S L O W being the operative word.]
But 9 hours later it looks like the Save As process is about half done.
Another week and I might actually get this done.