How can I restore emails from a deleted mailbox?

I did something dumb this morning and deleted my 'Archive' folder in Mail. Don't ask, long story.

Anyway, I had a fully bootable cloned backup from yesterday so I searched around and found where the mailboxes were stored:

my user/library/mail/v2/mailboxes

So I move the Archive mailbox from my external hard drive to my laptop's hard drive and while a few of the more recent ones I moved there (before my backup yesterday) are missing, by and large everything seems to be there.

Except, I use MailTags and when it restored my messages, none of them have this metadata assigned to them anymore. So my Smart Mailboxes that utilize this data are empty.

I realize my question is difficult to answer because of the use of this 3rd party software, but I'd really like to find a way to get back to the data state I had prior to my dumb move this morning. Should I just move the entire 'V2' folder over from my backup, would that do it?

Worst case scenario I could restore my entire hard drive to the backup from yesterday, but that takes a long time and it's something I'd obviously REALLY like to avoid if at all possible, but if I can't restore this meta data, it's going to make my life very difficult in a number of ways. I appreciate any suggestions anyone has, thanks.

FYI, I'm running on a macbook pro with the latest version of Mountain Lion.