Not sure what the difference is. I found this in the documentation:
Updates topics generated from the selected Word document. Only the topics that have changed are updated.
Updates all topics generated from all linked documents including all Word and FrameMaker documents. Because all documents are updated, including those that you edited in RoboHelp, exercise caution when you use the Update All option.
Overwrites the current set of topics generated from the selected Word document. Use this option to force an update of the topics generated from the linked Word document after you edit the source in Microsoft Word. This option updates all topics including those that haven’t changed.
Force Update All
Updates all linked documents, including Word and FrameMaker documents, and overwrites all generated topics.
Which begs the question - is "Force Update All" the only option that affects linked FM files?
And why are the non-book files removed from my webhelp.hhc TOC when I select any of the updates?
The Update All & Force Update All will use your conversion settings to bring over all FM content again according to the settings for linked FM content. If you’ve edited the content in RH (& haven’t told RH not to allow it to be overwritten), the Force Update will clobber your edits. Where is your ToC coming from – did you tell RH to use the FM one or are you building it in RH? If it’s in RH & you update, it will wipe it & you’ll need to recreate it again. Normally, you use your FM ToC as the source (since your content is coming from FM).