BizTalk Pipeline deployment 

As promised a followup on the deployment problems that result from using pipelines in your project. The situation is simple and frustrating: The moment you introduce a send port and set it up to use any pipeline as part of your project, straightforward redeployment from Visual Studio becomes impossible.

You will only be able to redeploy again when you:

Now you can redeploy your application. You could export the bindings first, to make sure that you can restore the bindings again after redeploying. You will probably agree with me: Deployment should not be this difficult.

Next experiment: Put the pipelines in a separate project. Magic! Now you can deploy your project with a port containing a pipeline again from Visual Studio. This is actually a recommendation you can find in other blogspots. Simple conclusion: put all item types (schemas, maps, orchestrations, pipelines) of your application in separate projects, to avoid deployment dependency problems.