If an OSX update killed your system keychain, do the following:
1. Reboot 2. Boot in Rescue (Cmd + R after chime) 3. Open Terminal, enter `csrutil disable` 4. Reboot 5. In your normal OSX environment, backup following sources: /Library/Keychains /var/db/SystemKey 6. Open Terminal and enter `sudo systemkeychain -vfcC` which creates a new system keychain 7. Reboot to Rescue (Cmd + R) 8. Open Terminal, enter `csrutil enable` 9. Reboot
Oh, btw, this has nothing to do with your user’s login keychain, which resides at ~/Library/Keychains. The tilde marks the difference.