Consider the following scenario:
You have an existing application deployed that contains an orchestration that is bound to Send and Receive ports.
The Send port and Receive locations use non-passthru pipelines.
In this scenario, if you redeploy the same project from Visual Studio, the orchestration is unbound, and the pipeline settings are lost.
The fix for this problem is included in the following update of BizTalk Server:
Cumulative Update 5 for BizTalk Server 2016
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.