It turns out that Track Changes (Obviously turned on for my co-authors) completely messes with the labeling.
Source
Post Below:
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...
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