Problem with Search and References

I'm running into a strange problem in which my searches are no longer
working, or are working intermittently.  This is primarily for the File
search capability, but the References function seems to be broken as well.

I have a medium-sized Java project, a few hundred files, and I regularly use
the File search capability to look for a specific set of characters.  For
example, I knew that I use a literal string ("SAE") and I wanted to find
where it was used.  Easy enough, I brought up the search dialog, selected
the File tab, and keyed in the letters SAE and hit search.

To my surprise, the search returned zero matches.  I found the source member
manually, and the literal indeed was in the source, but it wasn't showing up
in the search.  So I typed a space (to force a change) and re-saved the
member and ran the search again, and this time the source member showed up
in the search.

Next, I saw a method call in the source member.  I wanted to see where else
this was called, so I simply double-clicked on the call (to select the
method name), and then did a right-click, References, Workspace.  I was
quite surprised to see zero references, especially since there was obviously
a reference right where I right-clicked!

I then did a right-click and selected Call Hierarchy.  That worked properly.
I turned around and did a References, Workspace again and it showed the
reference appropriately.  I did this to another method, same thing.

I realize this is very anecdotal, since I fixed of the problems, but it's
pretty straightforward: it seems as though the File Search and the
References use an index that has been corrupted or cleared.  Whenever I
actually re-save a Java source file, that source file's data is put back
into the index.  So my question is this: is there a way to force a complete
rebuild of that index?  I suppose I could export everything and re-import
it, but I wondered if there were another way around the problem.

My major concern is that if I try to do a refactor that I'll now miss
something (although it's interesting that the Call Hierarchy seems to work,
it's only the Search and References functions that are not working).

Joe