In one site which I went through carefully about 25% of the pages listed with a site: search were listed as supplemental results, but all of these werer old pages that were removed from the site 8 months ago and 301'd to the replacement pages.
All the new pages are indexed but rankings and traffic have dropped, and I have confirmed that all the 301s are working properly.
Looks like indexing problems to me and that perhaps they are going back to some old data as an interim measure.
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