My fix:
In plugins/bbpress/bbp-admin/bbp-metaboxes.php function bbp_reply_metabox at the //topics section I increased the value in ‘numberposts’ => ’5000′
The default limit of 250 was too low for my site.
My problem was similar in that I was also losing the connection between replies and their parent topics. In my case all the ‘parent’ topics were not being listed in the reply attributes box and so the connection was lost if we re-saved the comment.
The reason for this was the display limit of 250 for the topics.
My fix:
In plugins/bbpress/bbp-admin/bbp-metaboxes.php function bbp_reply_metabox at the //topics section I increased the value in ‘numberposts’ => ‘5000’