Missing Mail Subfolders After "Cleanup"

My searching function in my MacMail has become unusable. It would just sit there "searching". I finally had enough and went searching through the Apple Community to find a solution. I found one that suggested that I go to ~/library/mail and find my "V-folders" and delete the information in them. Then just rebuild my mailbox. So I did just that. However, now my email is missing subfolders that I had created that included MANY IMPORTANT emails that I have to find and recover. My last TimeMachine back up was two months ago, but I thought I could try going to those folders and recopying my "V-folders" back into the place where I deleted them. No luck. I've even tried rebuilding the mailbox after that. No luck. I'm panicking! I haven't emptied my desktop trash just in case the files I need back are in there somewhere. Can anyone help?!