When editing a conversation that has a document attached to it, you can select to remove the file by checking the 'Remove File?' box found on the 'Edit' form. When you select the 'Next' button to continue and then 'Save' (when you have finished managing your subscribers), your conversation will revert to a discussion, removing the original file but leaving the comment thread intact.
This allows you and your subscribers to still be able to view and interact with the discussion, and you also have the ability to add a new document to the discussion if and when you need to. If you wish to remove the entire conversation, simply select 'Delete' when editing and it will be removed from the conversation area and the related event.