There appears to be a slight problem with my Livecycle server with regards to documents suddenly disappearing!
After looking around, it seems that the documents are not deleted completely, but moved to another folder ('livecycle\content\lccs_data\contentstore.deleted'). Thankfully these 'deleted' documents can simply be moved back to the contentstore. Livecycle's ContentServices uses Alfresco, and I found the following with regards to this automated deleting of documents:
http://wiki.alfresco.com/wiki/Content_Store_Configuration
For now, I will attempt to remove this functionality (removing the StoreCleaner's listener, so no action will be taken), but I'm unsure as to whether removing the finding of orphaned documents could be detremental to the system.
Is there anyone who knows exactly why the system is incorrectly flagging files as orphaned and then removing them? In the Livecycle adminui I can still see the documents that have been deleted, so at least the UI is still holding references to them.