I'm sorry but I cannot help with restoring your e-mails. If they are on the server you should be able to download them again. Download all if I remember correctly but it is long while ago I used OE. System restore does not restore data. MSE is unlikely to have had anything to do with it. Compression of folders or an archive may have.
If you have valuable e-mails it is worthwhile creating a back up of them see click here