I've been building out a bunch of Win32 apps and I've run into issue with the Intune Management Extension not updating the .bin files in C:\Program Files (x86)\Microsoft Intune Management Extension\Content\Incoming after I've updated the .intunewin file in the Intune console. Even after several IME service restarts, re-upload content, etc. the file was not updating which means my changes were not reflected on the client. I had to give myself permissions to the .bin file so I could delete it, restart the service, the file was re-downloaded and then my changes were reflected.
How long is the Intune agent supposed to cache those files and how does it determine that they need to be updated? In my case, I only updated a single line in a powershell script inside the .intunewin package so the file size didn't change. Not sure how Intune tracks the package but it seems like there's an issue.