1. Yes. In your Auto Import configuration, "Options > Library & Folders > Auto-Import > Configure auto-import" set "Fix broken links" to "Yes (protect files on missing drives)"
What is probably happening is because you are powering down everything, when you wake the PC, the drives your media are on aren't immediately available, Auto Import runs, sees missing files, and removes them from the Library. This would be common enough if you were using a NAS, or external USB drive that is powered at the same time as the PC.
You could also stop Auto Import from running in the background, and just run it manually as required, but you lose some functionality that way. Uncheck "Options > Library & Folders > Auto-Import > Run auto-import in background".
2. No longer any need. Having Auto Import running in the background does this. It would be bad practice to force this with a command to fix the problem above, although it could be done.