I have found the important commands for installing the updates after deployment and agent installation. To search for new Windows updates, and this includes the software distribution in Windows Intune, you have to click on the button in Windows Intune Center. I have found a command to check for updates and a command to install the necessary updates. This could be handy to speed up the deployment process. Otherwise, you have to manually start the windows updates process via Windows Intune Center or you have to wait for 8 hours for an automatic installation. This is the button in Windows Intune Center.
This button is not more necessary if you use the command /updatenow and /detectnow
First, you need to find the executable. Open a command prompt and goto %programfiles%\ Microsoft\OnlineManagement\Updates\Bin\ In this folder you see omupdclt.exe.
Run for detect %programfiles%\Microsoft\OnlineManagement\Updates\Bin\omupdclt.exe /detectnow
You don’t get any information on the screen. For the detailed information you have to look at the logs in %programfiles%\ Microsoft\OnlineManagement\Logs\Updates.log or look at the systembar for this icon -> This icon means that the updates are detected and ready to install.
After that you have to run %programfiles%\ Microsoft\OnlineManagement\Updates\Bin\omupdclt.exe /updatenow.
This command will install the updates. You will get a pop-up of the Windows Intune Updates process bar. See screenshot:
For more information, you should check the updates.log in %programfiles%\ Microsoft\OnlineManagement\Logs\ or the eventvwr.