Using the l() function within a node description field
If you already turned old links into node/28 format, you don't need to touch your content any more. You can simply use Internal Links module that will replace it live with the current alias. The benefit is - with this module if alias changes, content still links to a node by node's id, and links stays valid.


  The Internal Links Title filter inserts HTML title attributes into links to other nodes on a site (if no title attribute already exists) using the linked node’s title as the HTML title attribute’s value. It also replaces href values which are in the “normal Drupal path” form (e.g. ) with a URL alias, if one exists.


Emphasis mine.