When some large files are being written in Microsoft BizTalk Server, and the SFTP Adapter poll is running at the same time, the SFTP Receive Location transmits the files incorrectly.
This issue occurs because the SFTP adapter polls a file before the file is fully written into the polled location. The file is identified and set to zero-length. Because the file is polled, the adapter deletes the file. If an attempt to delete the file is completed before the file is fully written, the delete is retried until it's successful.
Cumulative update information
BizTalk Server 2013 R2
The fix that resolves this issue is included in Cumulative Update 1 for BizTalk Server 2013 R2.
BizTalk Server 2013
The fix that resolves this issue is included in Cumulative Update 3 for BizTalk Server 2013.
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.