Shaun, I know there was a bug in Drupal's import facility that is probably the cause of the loss of all the formatting of old posts (specifically probably a linefeed/CR type issue. Given it is possible to delete posts/threads. Might it be worth considering whether you could delete all the lost format posts and re-import them; assuming that old bug has now been fixed?
I don't know what caused the loss of all the old links, so any info about that might facilitate inspiration especially if it is connected with the above so far intractable problem.
or put the old blatchat back online read only so we can at least use it? I know several people have offered the resources for this (me included), so curious why this has not been done. It always helps to understand the reasons for things, not least so we can all see if we can help in any way.
I ask now because of your work with the search facility, it looks like that should work nicely, which will garner hits on the old content.