We have a few win32 apps that self update. Sometimes we need to deploy a new update over the apps that self update. This is where the challenge is because if I use a version regkey value, then that value could get changed after a self-update. Same thing for product ID. If an installation is required and the Intune deployment detection method is set to the version regkey value or ProductID, then the installation will try to go through again. 

If the detection method is set to the existing of a file/folder, then I have to find something that is set to that version of the program. Otherwise Intune will say the application is already installed, but it didn't install the new update. 

My work around is to use a custom powershell script that searches for select criteria, uninstalls everything, then, re-installs the new update, should the self-updating application get stuck or hung. 

Does this make sense? I'm happy to provide further details if needed. I've also attempted to work with the program owner, but my efforts appear to not go anywhere.