Help!! I am in SERIOUS trouble here!

Summary of set up :

Kingston 8gb USB Thumbdrive running Portable apps
Thunderbird 3.1.7

Summary of problem

OK, so my PC decided to spectacularly crash on Xmas Eve (date not important!), and after a quick reboot of the PC and successful re-start of portable apps and Thunderbird Portable 3.1.7 I noticed ALL of my work emails going back from January this year (2010) are missing.

I have 2 main inboxes :
Work - Collecting mail from work POP server
Home - Collecting mail from personal Gmail

Apart from the above inboxes I also use local folders for downloading old emails from other random accounts I no longer use (hotmail etc) but still like to keep an eye just in case someone still contacts me.

My Home email folders (and emails) are all still there and there is no problem with that folder, but my Work folder is empty, and I mean EMPTY!!

Until the crash my folders were set up as follows :
WORK
> Inbox
> 1001 - January 10
> 1002 - February 10
etc

> Sent
> 1001 - January 10
> 1002 - February 10
etc

Now, post crash ALL the mail in both my inbox and sent items (about 3 weeks worth) is gone as well as all the subfolders for each.

I looked in my drive folders (Data >> Profile >> Mail >> pop.xxx.com and there is NOTHING in there..

Now, what I find strange is my Thumbdrive is still saying that I have 6.59Gb of used space (same as before the crash), which I can only assume means the folders are there somewhere (no??)

I have run a checkdisk - nothing.
I have tried using a USB file recovery software tool and after 28 hours of running it gave up and crashed
I have copied the entire Thunderbird folder to another thumbdrive but was surprised (maybe not) that only 505mb transferred, which makes me assume the folders aren't trapped in the Thunderbird folder but some kind of trash file - no?

So, where are they?

PLEASE can someone assist with this, as I stand to receive a real kicking from the boss if I tell him that I have lost everything from this year.

As an aside, I DO have a back up of sorts, but I haven't updated it for about 3 months (isn't that always the case!) which is just a drag and drop of the Thunderbird folder onto an old HDD... would that help in the recovery or can I use something from that copy to recover everything?

Your assistance in the matter would probably save my job!

Paul