When an SFTP send port receives a zero-byte message in Microsoft BizTalk Server 2013 R2 or Microsoft BizTalk Server 2013, the SFTP adapter cannot create a zero-byte file in the SFTP server. Therefore, the empty message is lost in the SFTP send port.
Cumulative update information
This issue was first fixed in the following cumulative update for BizTalk Server:
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.
For more information about the service packs and cumulative update list for BizTalk Server, see KB 2555976: Service pack and cumulative update list for BizTalk Server.
For more information about BizTalk Server hotfixes, see KB 2003907: Information about BizTalk hotfixes and cumulative update support.