tedster - 11:12 am on Dec 21, 2008 (gmt 0)

When your server goes down, you are temporarily out of the index until googlebot confirms that your server is dependable again - that's not a penalty. What you do is up to you, but if you are understanding the situation correctly I'd say a server change is the best idea. You can return a 503 status until the files are in their new home.