Closed Eclipse. Deleted all folders under bad "workspace" workspace
folder. Copied all folders from "good" "workspace2" folder into
"workspace" folder. Restarted Eclipse. Everything is now visible in
"workspace" same as "workspace2". So the problem must be in some data
within the workspace subdirectories at least, not global to the Eclipse
installation.
I didn't keep a copy of the deleted bad workspace so can't do any more
analysis, but don't really have time. I hope the Eclipse developers can
gives us some kind of a workspace repair or rebuild tool or more insight
into this problem so we don't have to clone our workspaces from scratch
periodically.