Michael,
I had in the original script to at least let the user know that there are broken links (we still had some mxd's from two and three servers ago!!). It would alert the user that there was a problem with certain data and then continue on.
Once the db was turned off, ALL feature classes were broken links and it wouldn't change anything at all.
I was mainly putting the info on the forum as a warning to others to run these types of scripts before the db is turned off so that it has a better change of running properly. With any luck, in future versions of AG and ArcPy (we are running 10.0) they will handle stuff like this better because sometimes you don't have the choice of being able to turn a db back on - especially if the server died completely and you had to move the db to another server. You also don't always have to option of naming a server the same name.
So for now, I've turned the db back on for a few days to allow for the users to get to the directories with many mxd's (several with over 100) changed over. Any others that are looked at later, will just have to use the repair data source option within ArcMap.
Thanks.