I'll repost a comment I left:

Your first problem is that you started deleting stuff from a folder that Apple now deems wise to hide. With all due respect, why on earth would you start from the ~/Library folder? Why not delete these from the Mail client?

You can even "backup" from inside Mail.app. (Right click a folder > Export) Also, if you really want the Library folder, you can just go to Finder > Go > (Hold option) Library

There are real criticisms to be aired, this is not one of them.