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Few years ago we had our page under a subdirectory of the provider; something like:
We registered our dominion:
The pages of our new dominion are still on the old provider server. What we changed was only the registration of our dominion. When we modify our pages we can find the modified pages on both the old and the new dominion.
The problem is that some search engines (Altavista and Intomi) list our index page with those two different addresses (the old dominion and the new one that are the same: in fact we have only one site): we have two different listing with only one site.
This could be an advantage but in fact it seems that sometimes they are deleting what they think are duplicate pages and usually they delete our new index (new dominion) page that is the page that has the most link popularity.
So that we go up and down on the listing for our targeted keywords.
What can I do to force these engines to list only the new dominion?
You can try emailing the search engines themselves, and explaining the situation. (I've had terrible luck with AltaVista, but other people have had great luck with getting technical problems resolved with Google...)
Yes, our new (www.domain.com) address leads to the SAME place as our old (www.host.com/domain) address! We haven't changed hosts.
No problem with google and very few problem with Inktomi since we have several paid registered pages.
The only problem concerns Altavista. Our main page was ranking to the top for targeted keywords (without spamming or using tricks) because there are a lot of themed sites linking to us.
Maybe Altavista is not so stable in these days: we noticed that we have pages ranking fine for same targeted keywords, only because we have those keywords in the "keyword metatag"; this applies for keywords in capital letters for example.
What it is curious that this apply mainly for the main page. Most of new dominion page are listed fine. Doing a search on Altavista using the feature "More page from this site" related to the old dominion shows me two times (two listings) the main old dominion pages: the page of few months ago and the page with slight modifications of few weeks ago.
I have the impression that Altavista is using different databases because sometimes I can find both the new and the old dominion, sometimes only the new one, sometimes only the old one.
However, if AltaVista is your only major concern, you would probably be better off just waiting for their database to become stable again before you try contacting them about it. It may fix itself.