Symptoms:
Outlook 2016 is only pulling emails from subfolders. Inbox is empty.
Solution:
Check if the path to your Inbox is set in your Outlook 2016 settings.
To set the root folder path for your IMAP account:
File-> Account Settings-> Account Settings…
Double click on your IMAP account.
Button: More Options…
Tab: Advanced
Option: Root folder path
Setting this to “Inbox” will do the trick.
Click OK to close all of the opened dialog boxes.