MicrosoftI'm just doing some testing for repairing the Taskbar... You're going to need to manually generate a list of all applications and create the shortcuts back in the start menu. You can find most (but not all) of the shortcut paths here HKLM:\SOFTWARE\Microsoft\Windows\CurrentVersion\App Paths\
Once you've created the shortcuts, you can just copy the .lnk files back into the following path C:\Users\<username>\AppData\Roaming\Microsoft\Internet Explorer\Quick Launch\User Pinned\TaskBar and the taskbar will correct itself. If you copy .lnk files that the user hasn't previously pinned, it will only show/correct their pinned taskbar shortcuts and explorer appears to ignore all of the other .lnk files that were not pinned.
I'm thinking, we can run a script from Intune in the user context to copy shortcuts into their %AppData% directory? Alternatively, we could maybe run the script as admin context, but recursively list the C:\Users\ directory and inject all the shortcuts back into everyone's taskbar. Not sure the best approach yes, but I will be spending my afternoon scripting and testing, but just thought I'd pass the information on to someone else if this helps.
https://endpoint.microsoft.com/#view/Microsoft_Intune_DeviceSettings/DevicesMenu/~/powershell
