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So unattended updates are configured to run at every shutdown, OK.

But until that point, a GUI comes up on Ubuntu 18.04 desktop saying that XY needs to be upgraded.

The big Question: How can we disable the GUI pop-up Window to the users?

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Open Synaptic Package Manager then go to Settings -> Repositories -> Updates and uncheck Check for updates.

I'm not sure how you have unattended updates set up, but if it's using a cron job then this should work fine.

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