It depends on where these links are and what consistent patterns they have. For a start you could add a redirect in your htaccess, eg.
Redirect /component/content/138-publications /publications
So that the link example you provided would go from
But this depends on all the 404ing publication links matching that pattern. If you need to run some search and replace on the content table of the database then you should post some examples of how the links look therein.