I know there has to be a simple was to fix this...but my brain isn't working very well right now.
Here's what I did, what happened:
Set up a directory in a site, and built a new site within that directory. Everything was working fine going to mysite.com/newsite/.
Was happy with it so I got a domain name and just pointed it to that directory on my hosted account. Did that yesterday, domain propogated today. Got home from work went to newsite.com and all the images were missing. I had set them as "Root" relative. Then I realized all my links were "root" relative also! Went thru my site and changed all images and links to "document" relative. Problem solved....I thought.
Checked my server logs and saw some traffic across the original pages for mysite.com/newsite/. Traffic came from google, yahoo, and webcrawler. I'm thinking....wow...just put this stuff up over the weekend and it's being found!! Well, I go check the search engines, they of course had indexed mysite.com/newsite/ Click the links...low and behold the images and links were messed up since I had just changed them to 'document' relative.
So the linking will work as 'root' at mysite.com/newsite/, but needs to be 'relative' at newsite.com pointing to that same directory. Only solution I see is to copy the /newsite/ directory to a different directory and point the new domain there, and fix the links for each individual issue.
The concern here is over the fact that the pages were picked by the search engines so quick. I dont want missing links showing up when I know I'm getting traffic.