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Anyway, had to move to a new server about 2 months ago, and decided to rebuild/code pretty much the entire site. Idiot me, I created the new version on another G-visable domain (basically duplicating content) .. G dumped the main site ironically the very day before I was to move to the new dedicated server.
Thought I'd suffered a manual removal or some severe mechanical penalty. I wept and cursed .. and appealed to Google for clemency.
As of 3 days ago, the site is back in Google, with the "new" pages being crawled like the good old days. And traffic climbing back up nicely.
Still don't know if it was a manual or mechanical (for myriad reasons) penalty .. or a Google glitch .. my experience with other sites I've been prone to tinker with a bit too much is .. G-bot enjoys new pages, but not so much what amounts to a new SITE with each visit.
My experience anyway ..
At any rate .. I simply let the "new" design/pages for the "old" site be as they were .. pages have begun to reappear .. not all of them at once (it seems as if G is re-crawling everything for what it thinks is the first time) .. page rank appears to be fairly robust (not quite what I had before .. but much much much better than a sandboxed new site).
My hunch is there was some combination of triggers that flipped an automated "dump this site" filter on the new and improved Google .. the "Google you goofed" emails I'd sent may have helped get it back in, but mayby not. - G keeps us in the dark. And what works in the morning might be obsolete by the afternoon!
Anyway, I'd build your site the way YOU think it should be buildt, with the pages YOU feel would best represent your company/products .. and let the SEs figure out how to deal with it. - And be prepared for a campaign of patient reinclussion request emails if you don't see Google bot in your logs. - Once you see the crawler, that's great, you just need to wait a few more weeks and your pages should begin appearing in the SERPs ..
Which brings me full circle to my prefacing comment .. I'm really not sure if what I *think* I know is true or not .. too many unknown variables at work. But wishing you luck during what I know is a painful period of compromised profit.