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As to why, well that's just philosophy, but look at what appears to be the original target of the supplemental index: garbage/scraped/duplicate pages. You want that stapled on the front of (any version) of your main page?
Indeed - me neither.
>>>>Has anyone ever snapped back from this or reolved this?
Yes, although it seems to be luck of the draw. There does not seem to be a general fix.
301 the non-www to the www and you may get lucky.
The issue here seems to be on the Home Page only, the non-www homepage is supplemental, and the www. home page is fine, it has been like this for over a year, and the time assumption is solely based ont the Google cache of Jan 2005, however the sites rankings weren't noticed lost till around Jagger, so no one ever noticed the non-www. It has been 301'd since Oct, with no pickup in rankings, only downward shifts. Although Google Sitemaps claims the site ranks for terms it does not appear on from a manual search, some are there some aren't.
It holds some top 20 rankings for very competitive terms, those are drops, but the really non-competitive terms and regional terms are all gone. Its hard to be 100% sure that the non-www is the reason and not Jagger.
The base tag may help here too, putting <base href="http://www.domain.com/"> on all pages, but your internal links must then all start with a / OR include the full domain.
During Jagger my rankings plummeted then regained partial ranking in Dec, then dropped once again in early Feb. I have not recovered from the Feb. downturn as of yet and have been sliding even further down.
There is a specific search that I can do that should bring up my index page as the #1 result. The supplemental version is #1 and the current correct www version is listed at #10. Both version are appearing for the same search with the supplemental ranking higher. That should not be happening.
I am trying to be patient as possible with the new infrastructure in place and all that is needed to fix issues. It is very difficult though to accept the timeframe as how long this might take to fix. Until that supplemental page is really deleted (not hidden), I do not know what to do but wait.
I also do not get fresh tags anymore. I have not seen a fresh tag next to my listings since October of last year. Before Jagger, I got fresh tags all of the time.
Matt Cutts indicated at the end of March that a Supplemental "refresh" would occur near term. Has anybody seen anything to indicate that this has taken place? He also indicated back in Jan that any page that is supplemental that is 301 would be removed the next time the supplemental bot came around.
I have not seen any of this take place yet and do wish that they would get to it.
It was suddenly mentioned a few months ago (by Matt Cutts or GoogleGuy), but when previously chatting on similar topics, it not been mentioned at all.
At the moment I am guessing that it is vapourware.