- In Logos 5, enter "update now" and let the check for updates run; ...
- As soon as the "Logos is downloading" notification appears, close Logos 5.
- The Indexer will continue downloading; when it finishes, it will notice that Logos 5 isn't running and will prepare and index your library.
- When you start Logos 5 in the morning, everything should be ready to go.
Bradley posted the above in another thread ... I have experimented with it, it works from downloading (0-100%), preparing (stage 1-3) and indexing (0-100%). 
- The process that Bradley mentioned works if it is ONLY Updating of Resources
- We are still required to manually click "Install" when you hover over the Logos Icon on the menu bar (Mac) or Taskbar (Windows).
Would appreciate if Logos can consider to auto restart for the above mentioned, even if updates includes software updates. I am using Logos Bible Software 5.1b SR-1 (5.1.2.0079) for both Mac and Windows.
Thanks.