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So I am curious if it might have to do with how you are deploying patches? Are you just running the Microsoft tool or using another method?
You might consider scripting the process with Powershell; and then before running the scripts on your machine Stopping your services then doing a reboot after the patches complete letting the services restart.
I work in government so staff in the server unit set up this and script windows updates for all servers. I can't even turn off the windows updates sadly, but I will see if they can also script to shutdown services before the windows update thanks.