Whenever problems strike after a macOS update, there is always the universal panacea: install the latest Combo updater. Time Machine not backing up hourly? Troubled by repeated prompts to enter your user password? iCloud Drive playing up? Simply install the latest Combo updater.

As I have explained before, there are good reasons why doing this can fix various problems. When you install an incremental or Delta update, e.g. from 10.12.5 to 10.12.6, only those system components which have changed in that update get replaced. If older components of macOS have somehow become damaged, then those damaged files remain, and can result in odd problems.

There’s also the chance that the latest updater didn’t ‘take’ fully, and some of its updates weren’t installed properly, or were not installed at all. As macOS protects all its files and apps using SIP, you can’t (readily) use Pacifist to re-install just some components like the Mail app. Worse, many apps like Safari are intimately connected to large swathes of macOS, like WebKit.

A Combo update replaces all the components which have changed since the initial major release, which is inevitably greater. A Combo update is therefore more likely to fix problems which have arisen because of damage to macOS components. It can also rectify incomplete updates: although these should never happen, they sometimes do, leaving subsystems in a mess.

The macOS Sierra 10.12.6 Combo update is available from here as an offline installer. It is easy to use: once downloaded, open the disk image to mount it, and run the Installer package.

But the job is not quite complete: there are a couple more tasks which you need to do before this refresh update is done. First, you need to open the App Store app and check for updates, in case applying the Combo update has reverted any regular components that came with it.

There is also the interesting issue of Apple’s XProtect and other security configuration files, which are normally updated silently. Look at the list of updates installed by opening About This Mac, clicking on the System Report… button to open System Information, then selecting the Installations item in the Software list at the left. List the items by Install Date by clicking in that header, and order them from most recent at the top (click a second time in the Install Date header for that). Until you see a list with those normally silent updates, your Mac may be vulnerable.

This is because the Combo update reverts XProtect and other configuration files to those which came with that update, not the most recent. To bring that protection up to date, you now need to force those to be updated, rather than leave your Mac to catch up in its own good time, which may be during the next night.

There are two methods which should force those to be updated: you can open the App Store pane, uncheck the Install system data files and security updates item, switch to another pane, then back to the App Store pane. Turn that item back on, then click on the Check Now button below.

That may not always work. If it doesn’t, open Terminal and enter the following command from an admin user account:
sudo softwareupdate --background-critical
press Return, then at the prompt, enter your admin account password. Terminal will then report
softwareupdate[1587]: Triggering background check with forced scan (critical and config-data updates only) ...
and in the next half hour or so, the updates should be downloaded and installed. Check by opening System Information and looking for those updates, which will be more recent than your macOS Combo update.

Soon after a macOS update, there may not be any ‘silent’ updates to install, though. You can check this by browsing my list of those silent updates here.

Finally, what should you do if you have problems after upgrading to a new major version of macOS like High Sierra 10.13, or after its first minor update to 10.13.1?

For major upgrades, the only option is to run the upgrade installer again. These have a habit of deleting themselves immediately after you have upgraded, so make a point of tucking a copy away before you run that installer. Even if you have a very high-speed internet connection, large installers like that are worth keeping around. You can use them to make bootable USB drives and more, as well.

For the first minor update, the Combo and Delta updates are identical, so you should try the Delta update as if it were a Combo. If that doesn’t help, you might need to go back to the original major upgrade, then apply the Delta to that.