Settings different after update

I ran the security update while I was sleeping last night, and this morning my settings have changed. My wallpaper is gone. Notifications are on for apps, where, previously I had them off. I’m sure I’ll discover more later today as I’m using my phone, as this has happened after other updates in the past. Then I have to go through and put all my settings back where I want them. Why does this happen and how do I stop it from happening in the future? I’m doing nothing else to my phone; Only allowing the update to occur during my sleeping hours.