You get the following error when you do a BTDF deploy.
x does not belong to the same application as “Y” or its references.
Full example of error
Information: Importing bindings "C:\Users\...\Projects\MyEDIProject\MyEDIProject.Deployment\PortBindings.xml" into application "MyEDIProject" in BizTalk configuration database (server="MyServer1", database="BizTalkMgmtDb")...
Error: Failed to update binding information.
"Microsoft.BizTalk.Edi.DefaultPipelines.EdiSend" could not be bound to "sp_MyProj_Process_EDI_File". The artifact "Microsoft.BizTalk.Edi.DefaultPipelines.EdiSend" does not belong to the same application as "sp_MyProj_Process_EDI_File" or its references.
The pipeline is in a different project. When BTDF deletes your project and redploys it, it loses the project references. You must add the project cross references in the BTDFProj file, as shown below.