I used Titanium Software's 'Maintenance' app to rebuild the Spotlight index, and clean the System and User caches, and clean Obsolete, temporary, and Recent Items. Still no joy...
The pointers to these 'dead' folders appear under the Favorites section in the Where drop-down menu when using Save As... All my Sidebar links in Finder windows are functional.
I had an alias to one of the 'dead' folders on the Dock, and it retained its custom icon after the partition/data restore operation, so I didn't think anything of it until I tried to use it, and nothing happened, its invalidity was revealed. It was easy to drag this dead item off the Dock and drag the 'new' folder (same name, same custom icon) onto the Dock.
Viewing the Where drop-down list in the Finder Save As..., I tried dragging the dead items out (with Cmd, Opt, and Cmd-Opt keys also), but they're adamantly untouchable. If a dead item is clicked, nothing happens, the destination for the save remains unchanged.
Perhaps these dead items will magically disappear down the road, but I would like to know how to destroy them. I looked in various plist files etc. but didn't find anything that seemed relevant.