Well i was thinking of ways to deal with actual content being lost. If it's an indexing problem instead, dang, wish i had some idea but i've never used Dreamweaver.
When i'm not using good ole notepad, i'll sometimes resort to Adobe Go-Live for complicated table layouts or to set up complicated Javascript stuff just to see how it looks, then go back later and boil all the bloated code these programs generate down to some very basic stuff that achieves the same results.
From the reviews i've read in a more powerful program than Dreamweaver, but in my experience it's extremely buggy, but since i know by now how to bludgeon it into submission i still resort to it rather than DW when i have to, so i'm still ignorant about DW.
I've seen this kind of thing in Go-Live twice before; once my boss at the time had deleted the sitemap file and when it was recreated it was somehow created one folder up or down in the hierarchy from where it should be.
The other time was when a server we were using revamped their structure without telling us and totally f*cked every link on our site. It was that way for a couple of weeks until somebody compalined and we checked it out ourselves. Had to hurry to upload everything again into the new structure and change all the cgi/perl scripts that contained server paths in them. Argh.
If you have a standalone FTP program like WS-FTP or Cute or wheatever it's called, maybe you could send some of the pages up that way and see how things work; it might reveal how the links are wrong in DW...