We're using BizTalk 2013 and we have several resources that import web services to use its schemas and ports. Some of these ports are used at the same time in several of our BizTalk applications. In administration, each of these ports is connected to the same physical port, so the scenario is several logical ports from different orchestrations and resources connected to the same physical port.
With all the system well configured, we import the MSI of some of this applications (only MSI, not bindings included) and after the import finished correctly, if we check the physical ports shared, pipelines configured (XmlReceive) are lost and pipelines PassThru are set.
Making some digging, when you make a MSI import, some binding files are created in URI .\AppData\Roaming\Microsoft\BizTalk Server\Deployment\BindingFiles for all the resources, I guess to get the current situation before import and apply it again after. In the first binding file created, pipelines are well configured for the physical ports, but in the next ones PassThru pipelines are set in the ports. After the MSI import ends, seems like the port gets pipeline configuration from some of the files with PassThru.
Of course if we make an export/import binding before/after the MSI import, it works perfectly. But it seems more a workaround than a final solution.
It will be great know if some of you have this same problem and/or some ideas where I can dig more to avoid this problem.
