Issue: Unable to get Skype for Business missed call notification in Outlook and missed call alert.
I think there is bug in Office update November 10, 2015 (KB3101496) due to that Missed call notification cannot saved in Outlook 2013 and cannot see missed call alert under Skype for Business client.
Also in some cases your Skype for Business client crash frequently after applying this updates.
As a workaround you can uninstall KB3101496. After installation of this update Missed call notification shows in Outlook and missed called alert in Skype for Business client. Also Skype client stops crashing.
If you want to go back to previous version of Office then use below script.
"C:\Program Files\Microsoft Office 15\ClientX64\officec2rclient.exe" /update user updatetoversion=15.0.4745.1002 updatepromptuser=True forceappshutdown=True displaylevel=True