How to restore emlx files in their rightful place (Mail.app)

Question

This might be the wrong place to post this, but I don't really know where else to try. The story goes like this.
My girlfriend uses mail for business and personal, but never filed any of her emails away. There they were, 2000+ emails all in one folder. I don't know why, but it drove me nuts and one evening I tried to file them all away, with hideous consequences.
I somehow managed to create two folders with the same name. I then tried to delete the empty one, but of course, as Murphy's Law dictates, the app deleted both of them.
About 60% of her emails were deleted. No undo, no look in the trash, nothing.
Boy was I in trouble. So I shelled out $80 on FileSalvage, which managed to get them all back. But of course now they come in a single folder with different names (1.emlx, 2.emlx , rather than 6378.emlx etc etc)
Now I've got them in a folder on the desktop, and I need to find a way to get them back where they belong. As the details of where they used to be are still stored in the "envelope index", is there a way of launching terminal and looking at the data in the sql lite db here? Then making some sort of applescript that will save them in the right places?
I'm fairly au fait with applescript, but have no way of finding what the previous names of these files were.
Obviously I've learnt my lesson - so no "should have backed it up" responses, please! Girlfriend still very annoyed. And it all happened 6 weeks ago!

Answer 1

What makes you think this could be the wrong place to post about your problem? I wish all posts here where as on-topic as yours.
Mail has some bugs and glitches when it comes to manage mailboxes. If you see strange things happening when doing so, quit Mail and make a backup of the ~/Library/Mail folder before trying to "solve" the problem by deleting anything.
Back to the problem, verify/repair the disk first (not just permissions), as described here:
The Repair functions of Disk Utility: what's it all about?
After having fixed all filesystem issues, if any, and making sure that there's enough space available on the startup disk (a few GB, plus the space needed to make a backup copy of the Mail folder), proceed as follows if you want to re-create the index:
1. Quit Mail.
2. In the Finder, go to ~/Library/Mail/. Make a backup copy of this folder, just in case something goes wrong -- e.g. by dragging it to the Desktop while holding the Option (Alt) key down.
3. Locate Envelope Index and move it to the Trash. If you see an Envelope Index-journal file there, delete it as well.
4. Open Mail. It will tell you that your mail needs to be "imported". Click Continue and Mail will proceed to re-create Envelope Index -- Mail says it's "importing", but it just re-creates the index if the mailboxes are already in Mail 2.x format.
You can import the *.emlx messages back into Mail by creating a folder with an .mbox suffix (e.g. Recovered.mbox), then a Messages folder within that folder, and moving all the *.emlx messages to be imported within the Messages folder.
In Mail, do File > Import Mailboxes, choose Mail for Mac OS X as the data format, and follow the instructions to import the recovered messages. Note that Mail wants you to select the folder that contains the *.mbox folder, not the *.mbox folder itself.
Note: For those not familiarized with the ~/ notation, it refers to the user's home folder, i.e. ~/Library is the Library folder within the user's home folder.