We seem to have an issue with Outlook 2016. We run Windows 10 x64 as our OS with Office 2016 Standard (x86). The handful of machines that we deployed the fall creators update to so we can test it, we have noticed no longer receive desktop alerts for new incoming email in Outlook. With that we've found that Outlook is missing from Notifications and Actions. If we do a reinstall of Office 2016, it reappears and the issue is resolved. We however, cannot do that for nearly 100 machines.
I don't know if this will help shed any light on the issue, but we deployed office using the built-in customization wizard with some minor customization. The only one i noticed that could be relevant is we opted to move the Office 2016 apps under a start folder called "Microsoft Office" so it matched the layout of our previously used Microsoft Office 2010 suite (simplifying things for our end users). When we tested the reinstall we did a standard non-customized install, and have not had a chance to test with a reinstall of the customized package as of yet.
If anyone could offer any suggestions or assistance that would be very helpful as i cannot find much relating to this in forums nor have i been able to find a way to resolve. As of right now it is holding up our ability to deploy the fall creators update to our end users.