Update: after numerous restarts of Logic and the Macbook I decided to try Logic's "Download Additional Content" feature in the Logic Pro menu. I selected "Logic Pro & Mainstage Additional Content" hoping the missing samples and instrument had inadvertently been moved into those files by Apple.
That may or may not have been the case, but now after having installed that content and restarted Logic the missing files are apparently no longer missing. I still need to rescan AU devices to get rid of that synth plug-in, but the main problem appears to have been solved.
Thanks for looking! I hope this record of my experiences with this issue will help someone else in the future.