If it's base files, I would download the El Capitan installer again and run this over my current install.
If it's your User's folder, we can try resetting your Mail files.
Make sure you have backup first.
If you have POP accounts or mail stored under "On My Mac", this will take additional steps to recover.
In System Preferences > Internet Accounts
Uncheck Mail for each account.
With Mail quit....
Go to your User's Library folder. (see below)
• Go to Containers. Drag the com.apple.mail folder to the Trash
• Go to Mail folder. Rename Mailxxx
• Go to Preferences. If you find any com.apple.mail.plist files, delete these.
Log out under the Apple in the Menu bar
Log in
Empty the Trash
In System Preferences > Internet Accounts, check one email account. You want to do this for one account at a time.
Open Mail.
Verify the account is working and you are getting mail sounds.
Add additional accounts and test after each account.
If you still don't have mail sounds, it's possible there is another file that is corrupt that is not in the data we reset.
Show User's Library
The User's Library folder is hidden by default. To unhide: Select the Finder in the Dock. Under Go in the Menu bar > hold down the Option key and you’ll see the Library.
Finding the User Library Folder
http://www.takecontrolbooks.com/resources/0167/site/chap11.html#FindingtheUserLi braryFolder