We can modify the receive and the send pipelines from an SQL script.
First of all, we need to know the pipeline Id value, from the BizTalkMgmtDb database:
select Id from dbo.bts_pipeline where [Name] = '<Pipeline Name>'
Then we can modify the pipeline from wichever send port or receive location:
update dbo.adm_ReceiveLocation set SendPipelineId = <Pipeline Id> where [Name] = '<Receive Location Name>'
update dbo.bts_sendport set nReceivePipelineId = <Pipeline Id> where [nvcName] = '<Send Port Name>'
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