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With a certain search engine, there are just too many issues right now for new sites (sandboxing, etc.) that you would do well to keep your existing site in place until the new site gets established.
BTW, welcome to WebmasterWorld.
Hope this helps :-
JohnP
Our homepage has the most traffic and we will be adding more content and more keywords to it. Are there any possibilities of our rankings going down from just that?
Build the new site and put it on a sub-domain with full A record. You can submit it and tinker with it and it'll only cost you the time spent, and won't put your existing site at risk. From what you write it appears to be a fairly major re-build of the site, so there should be no conflict between the two in terms of what the search engines see. When the new site has better ratings than the old one, just put it on the main domain with a 301 re-direct on the sub-domain and you'll be safe.
There's lots of ways to do this job, but it's important to not disturb the original site while you mess around and build the new one. It also depends on what access you have to the server - for doing stuff like sub-domains, redirects, etc.
Hope this helps.......
Don't forget to add www.newsite.mydomain.com as well - both should have their own A records in the zonefile to make the two websites separate in SE's eyes.
So your zonefile will read something like -
mydomain.com. IN A 123.321.321.123
www.mydomain.com. IN A 123.321.321.123
newsite.mydomain.com. IN A 123.321.321.123
www.newsite.mydomain.com. IN A 123.321.321.123
I suggest that you make all your e-mail from the newsite go to a series of addresses with something that will allow you to see where they've come from. Addresses could be newsite_info@mydomain.com , newsite_admin@mydomain.com , etc. You'll be able to create rules in you local mail client to sort these from the usual@mydomain addresses. Once the newsite is in a position to take over, it's a simple matter to change the e-mail addresses - not forgetting to keep the old ones for those peole who send one e-mail a year (I wish!).
Hope this helps you along......
Slainte,
JohnP.