Mail stored files missing after system restore

[Sandy Scott]

I have had to restore my iMac twice recently using my TM back-ups and everything went smoothly. I recall after the first one being asked if I wanted to re-build my Mail database and I answered "yes" and it imported many files. I cannot recall if I was asked that on my last back-up and here is my problem:

I just noticed that for some reason, storage folders that I have recently used have all of the stored emails in them including quite old ones, but some important folders that I have not accessed in quite some time are totally empty and there were some important emails that I missed to save.

I am sure this stuff is residing somewhere. Can someone give me some guidance as to how I might find and restore my old mail storage files that are now empty? Thanks.