Consider the following scenario:
You use a custom receive pipeline or send pipeline in Microsoft BizTalk Server.
You update multiple schema assemblies at the same time in the BizTalk Server Administration Console.
In this scenario, the receive pipeline in Receive Location is reset to PassThruReceive pipeline, and the send pipeline in Send Port is reset to PassThruTransmit pipeline.
Note If you update schema assemblies one at a time, this issue does not occur.
Cumulative update information
The fix that resolves this issue is included in the following cumulative updates for BizTalk Server:
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.
Learn about service pack and cumulative update list for BizTalk Server.
Learn about BizTalk Server hotfixes and cumulative update support.