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I redesigned a total homepage. It was relaunched just 2 weeks before Dominque update....yes I think we can call it D DAY now. (DOOMS Day).
Anyway, all the URL's changed due of the redesign and new products were added (old ones removed and a custom 404 to redirect to the frontpage).
Now all the pages are gone from the index. The old ones, the new ones never indexed except the URL's that were kept the same. They are updated with the new information in Google (checked cache).
Googlebot before came along a couple times a week (yes I was not so lucky to see her every couple hours).
What did I do wrong?.
I have 1 tag in my 404 file that might be interesting.
<META NAME="ROBOTS" CONTENT="NOINDEX, NOFOLLOW">
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I was in the exact same boat, I had just redesigned our site before "Demonic". We were left out for over a month, altogether. I was worried that we were penalized. However, we came back and have most of our pages on all the data centers, only "ex, in, and cw" have our index page.
You may be lucky with the new system. It may not take so long, but you will be back. :)
...this tag would likely be better if it was just a NOINDEX (drop the NOFOLLOW) -- I would've thought you'd want to the robots to follow your re-direct to your homepage? -- then it would most certainly get indexed.
I don't think that having NOFOLLOW on your 404/re-direct page would would prevent the homepage from getting indexed though.