El Capitan Mail Alias?

I'm having the same issue.

My iCloud account completely disappeared from the internet accounts (System preferences), but I can't add it as I get an error that it already exists.

Some iCloud features are enabled though like the keychain or the photos. But mail, notes, contacts and my calendars are not synced 😟.

Haven't find any solution yet. Still working on it.

I don't think this is related to icloud. I have this problem with a google account. I just need to readd the aliases. Not a big deal

Although my iCloud didn't appear in the internet accounts in system preferences, it was visible in the dedicated "iCloud" section of system preferences.

I logged out there and logged back in.

It's now visible in the internet accounts section and my everything's synchronising correctly including mails.

Agreed. ALL aliases disappeared on the upgrade.

ONE caveat: the place to add them isn't obvious. It's the same place where it was, specifically:

Mail -> Preferences [NOT ACCOUNTS]

Second tab, Accounts.

First sub-tab, Account Information

Second entry, Alias.

I've logged a ticket with production support.

I followed advice below. I went to the icloud preferences in settings - then signed out of icloud completely. I deleted all the icloud files as it prompted me to do so, then I signed back in. My alais in mail app were restored properly when I did this. Working without problem now.