You need to
- Close out all instances of Word
- Re-open the file
- Move Word to a different window
- Click on Cross References again
Well, I was finally able to answer my own question. the answer might be helpful to others. It turns out that change tracking was wreaking havoc with figure and table numbers in the cross reference lists. I finally went through and selectively accepted changes to all the figure and table titles and the missing figures reappeared in the list.
The problem is that when they go away in the list, they also disappear in the document because the reference IDs become stale, I suppose. So now I get to go through and find all the places I inserted one of the references that disappeared and reinsert it. Thank you Microsoft...