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.
The above shows you how to add a “Project Reference” to your BTDF configuration file.