The posts rebake task should regenerate links too.

app/models/topic_link.rb

@@ -139,7 +139,7 @@ class TopicLink < ActiveRecord::Base
           if topic_id.present?
             topic = Topic.where(id: topic_id).first
 
-            if topic && post.topic.archetype != 'private_message' && topic.archetype != 'private_message'
+            if topic && post.topic && post.topic.archetype != 'private_message' && topic.archetype != 'private_message'
 
               prefix = Discourse.base_url
 

lib/tasks/posts.rake

@@ -3,11 +3,13 @@ task "posts:rebake" => :environment do
   RailsMultisite::ConnectionManagement.each_connection do |db|
     puts "Re baking post markdown for #{db} , changes are denoted with # , no change with ."
     i = 0
-    Post.select([:id, :cooked, :raw, :topic_id]).each do |p|
+    Post.select([:id, :user_id, :cooked, :raw, :topic_id, :post_number]).each do |p|
       i += 1
       cooked = p.cook(p.raw, topic_id: p.topic_id)
       if cooked != p.cooked
         Post.exec_sql('update posts set cooked = ? where id = ?', cooked, p.id)
+        p.cooked = cooked
+        TopicLink.extract_from(p)
         putc "#"
       else
         putc "."