I figured out a creative work-around, but is there an explanation for the problem.
I copied all the centroids to a new layer via a selection set, then I used Express to auto text number the centroids. The phantom centroids showed up as numbers with no text prefix, and I was able to delete them and replace the centroid with the proper text. Everything worked out. I tried file audit before this and that didn't help. Now, how do I remove the numeric suffixes easily?