Mail "aliases" gone. Mail.app refuses to allow me to correct it

Try a restart.

Do a backup, using either Time Machine or a cloning program, to ensure files/data can be recovered. Two backups are better than one.

Try setting up another admin user account to see if the same problem continues. If Back-to-My Mac is selected in System Preferences, the Guest account will not work. The intent is to see if it is specific to one account or a system wide problem. This account can be deleted later.

Isolating an issue by using another user account

If the problem is still there, try booting into the Safe Mode using your normal account. Disconnect all peripherals except those needed for the test. Shut down the computer and then power it back up after waiting 10 seconds. Immediately after hearing the startup chime, hold down the shift key and continue to hold it until the gray Apple icon and a progress bar appear. The boot up is significantly slower than normal. This will reset some caches, forces a directory check, and disables all startup and login items, among other things. When you reboot normally, the initial reboot may be slower than normal. If the system operates normally, there may be 3rd party applications which are causing a problem. Try deleting/disabling the third party applications after a restart by using the application un-installer. For each disable/delete, you will need to restart if you don't do them all at once.

Safe Mode - About

Safe Mode - Yosemite

My mail alias are gone after El Capitan update — and I ended up catching only AFTER my private email was exposed.

Please help fix this.

I'll ask the hosts to move the thread to El Capitan.

Try Mail/Preferences/Accounts /Account Information. Select an account, then go to Outgoing Mail Server (SMTP). From the drop down menu select Edit SMPT server list. Then set up a server for each mail account so that is associated with the e-mail address. Then go to each account and set that server as the Outgoing Mail Server (SMPT). You can click Use only this server if desired.

Mail/Preferences/Composing/Send to messages from - set to account of selected mailbox.

Same thing happened to me, but I have not downgraded to El Capitan. I went into Mail>Preferences>Accounts>Account Settings. At first, "Alias" for my iCloud account showed only my main account and none of my aliases. I clicked around between my different accounts (one icloud, two gmail and one exchange). When i went back to the main page, all of my aliases had reappeared. I know this isn't too helpful, as i have no idea what fixed the problem, but maybe clicking around will work for somebody else, too.

Some of you do manage finding a solution to it ?