Graphical message flow depends on tracking data. By default global tracking is enabled at BizTalk group level. However you suddenly notice that no data is being tracked by BizTalk., the first place to check is the Pipelines Tracking configuration.

In BizTalk Server Administration console tool, expand BizTalk Server Administration and expand the BizTalk group containing the pipeline for which to configure tracking. 

Do one of the following:

    To configure tracking for one of the default BizTalk pipelines, expand <All Artifacts>.


Click the Pipelines folder, right-click the pipeline, and then click Tracking.

Make sure that check boxes under Track Events are enabled :

biztalk pipelines tracking options

To enable tracking for messages make sure that check boxes under Track Message Bodies are enabled( this will pull message context and content in Graphical Message Flow Viewer) :

biztalk pipeline tracking properties

To track Orchestration events and messages enable tracking  for the Orchestration as shown below 

orchestration tracking properties