One of my clients wanted to change her domain name, and thinking i have done this before, and simply used some code from your book before, successfully i might add ( .htaccess code for 301 redirect), it seemed like it was going to be fairly straightforward. Not!
The first thing i did wrong - i think - was to purchase the domain name on a different hosting company, and find out that to transfer to the clients' host was going to take 60 days because of laws about that.
I still redirected the new domain name to the name servers of her current domain.
Then i get an email from the hosting company engineer, that he has set forwarding, but didn't think about it all that much.
A day later i think, well i didn't have to create any forwarding before, in fact that isn't what i want to do in any case, but what did he do?
When some one says they are going to forward i had presumed he meant that in the managing domain interface, i would see a forwarding, and possibly a mask, but that isn't what he meant.
He had created a new directory where the new domain files would go, and where i would download and upload the current file system and make my changes there. And he had also created a symbolic link, so if someone were to go to the original file system, they would end up at the destination link - the new directory.
Well i got fairly testy about that, thinking that now there is a confusion for the google index, and that he hadn't needed to do that at all.
But i seemed to have to go along with it, him having 22 years of unix experience after all, and me a lowly grunt. So now the files are in the new directory, with some changes to the files to reflect the new domain and all, and i have not yet submitted any xml sitemap or done any new accounting on analytics for the new domain name.
Basically i think that there are now split equity in any links, new index links that will be created for the new domain name and its pages, and the old links that will now linger and cannot get rid of.
What is my game plan now, and what should i do now to implement an effective seo plan for this new domain?
thanks in advance
eddie rosenthal

It won't affect the application. Its only affect the SEO.

exactly what i was saying. Everything of course works as it should. The redirect (301) that i wanted to do has been supplanted by a symbolic link, rendering the original directory unused. Google knows nothing of this however, so how do i redo the seo work that was done previously, when now it is unused?
My guess is that i have to erase the symbolic link, with the help of the engineers of the hosting company, and put in place the correct .htaccess directives for the proper 301 redirects. And what about the new directory with a duplicate set of files ( mostly duplicate, because their text has been changed a bit to correspond to the new domain name)...
OR
can i just take the .htaccess file in the original directory and add to it the 301 directives for redirect, and LATER REMOVE THE ORIGINAL DIRECTORY?
I need some expert advise here.

I just need some sort of consensus from the unix/seo experts around here to get the go ahead. I'm a punk who can't do anything more than follow directions, but which ones???