I worked on a project to migrate SharePoint 2007 to 2010. The 2010 site has a different URL than the 2007 site and I found lots of links in the top nav and left nav that had absolute URLs instead of relative ones. The absolute URLs were pointing back to the 2007 site. I decided to go against the grain and just execute an update statement in the content database to fix this. Alternatively you could go to Site Settings / Navigation Settings and fix this.
In my case the absolute URLs started with http://intranet.mydomain.com/ so I just wanted to convert to a relative URL. Here's the SQL statement to convert the absolute URLs to relative ones (grab the characters after http://intranet.mydomain.com and the / character that follows):
UPDATE [Content_Database_Goes_Here].[dbo].[NavNodes]
SET Url = SUBSTRING(Url, 29, LEN(Url)-28)
WHERELEFT(Url, 28) = 'http://intranet.mydomain.com'
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