It is 1-1/2 years later and there is only a lousy time-consuming bypass to the problem.
The real fix would be for Outlook 2016 (Outlook 365 desktop) to synchronize aliases with Outlook.com when a mail box is opened at the start of a session.
That doesn't happen. Instead Outlook 2016 only synchronizes aliases with Outlook.com when a new mailbox is added.
Outlook 2016 desktop won't detect additions -OR- removals to aliases in Outlook.com. It will only remember the aliases that existed when the Outlook.com account was originally added to Outlook 2016.
Here is the bypass, but it is lousy and time-consuming.
Go to Outlook 2016 desktop:
- Select File; Account Settings; Account Settings
- Select and Remove the email account concerned
- Shutdown Outlook 2016
- Restart Windows (i.e. reboot)
- Start Outlook 2016
- Add back the email account concerned
>> When adding the account back Outlook 2016 will detect the current aliases for the Outlook.com email account.
- Wait while the email account is added back
- Shutdown Outlook 2016
- Restart Windows
- Start Outlook 2016
- Add back all the view settings and message rules you had before.
I hope that helps. Hopefully MS will fix the root cause of this very common problem that many people have complained about.