Is it failing to undeploy because the agreement references one or more send ports in the application? If so, as a workaround I wonder if you could add another BizTalk app that holds only the send port(s), have the agreement(s) point there, and just add an app reference from your existing app to the new ports-only app. The ports-only app would stay there all the time. I suppose you'd have to leave the parties out of your existing app's bindings XML too.
As an alternative workaround, the Deployment Framework has a property named SkipUndeploy, and when you use the Redeploy Start menu command, the difference from regular Deploy is that SkipUndeploy=true. That mode doesn't remove the BizTalk app. You'd have to uninstall/install your MSI without running the undeploy step, and always use redeploy. It seems like you could run into some trouble if you made significant changes to the app between versions, although I don't have an example off the top of my head.
Thanks,
Tom
As an alternative workaround, the Deployment Framework has a property named SkipUndeploy, and when you use the Redeploy Start menu command, the difference from regular Deploy is that SkipUndeploy=true. That mode doesn't remove the BizTalk app. You'd have to uninstall/install your MSI without running the undeploy step, and always use redeploy. It seems like you could run into some trouble if you made significant changes to the app between versions, although I don't have an example off the top of my head.
Thanks,
Tom