Many thanks to the folks at NASA this week in Huntsville, AL. We sent round and round on this one in class today.
I was asked the question about deleting the default Sites Directory area and what affect that would have. Other than not being able to use the same URL, there shouldn't be much of an issue because a new Sites Directory can be created in the portal.
However, you should be aware that when the default sites directory is removed from the portal, the Add Link button in the Manage Sites to be Crawled list is also removed. If you create a new Sites Directory, this button is not rebuilt and there seems to be no way to recover the Add Link button without doing a restore of the portal.
FYI.
Bill English
Mindsharp