It's one of safest of these tools out there.
It suggests to make a restore point before changing any settings.
I would suggest you apply the recommended settings only and go from there.
I use it with the recommended settings, but changed for example the settings for Edge back to default because I didn't like to see "managed by your organization" in Edge. I had no problems with updates caused by this tool and like
@Arequire said you have to recheck your settings after an update.
O&O ShutUp 10 will show you what settings are changed after the update and you can redo them or accept the changes.