Have seen a few instances where the Skype for Business Plug-in will not run or start when you start Outlook. This will result in not seeing the New Skype Meeting selection from your Outlook Calendar.
There are a few things to check to get this Plug-in working correctly:
1. Goto File > Options > Add-ins and look at the state of the Skype Meeting Add-in for Microsoft Office 2016.
2. If the Add-in shows as disabled then at the bottom use the Manage drop down to select Disabled Items and click Go...
Select the UCAddin.dll (this is the Skype Add-in) and Click Enable.
3. If Step 1 showed the Skype Add-in under 'Inactive Application Add-ins' then at the bottom use the Manage drop down to select 'COM Add-ins' and click Go...
Make sure the Skype Meeting Add-in for Microsoft Office 2016 has a check box and click Ok. Restart Office and the Add-in should be back.
I did have one instance where the Skype Meeting Add-in for Microsoft Office 2016 check box would not stay checked. This was due to a corrupt Add-in. To fix this i was able to copy C:\Program Files (x86)\Microsoft Office\root\Office16\UCAddin.dll from another machine to the same location on the broken machine and replace the bad Add-in.
I also had to set the load behavior in the registry: