I use many application on BizTalk 2009. I have noticed many times that, after a resource add (.dll) in a random application, all the bindings (custom pipelines) of a precise application totally reset to an early previous state.
I'm really curious of why this happens. But I also need a solution to stop that behavior or resolve automatically this problem.
It happens because it tries to apply a cached binding after you have deployed. Sometimes it doesn't correctly update the cached binding and so a stale copy is used. As per below, clearing these cached copies out helps in the short term, but often it comes back.
From BizTalk Server: List of Errors and Warnings, Causes, and Solutions
Visual Studio uses cached binding files when deploying BizTalk applications. Removing these cached binding files will result in a ‘clean’ deployment that should resolve any binding related deployment errors. The files are stored in %APPDATA%\Microsoft\BizTalk Server\Deployment\BindingFiles. Clearing the contents of this directory should resolve any deployment issues related to cached bindings.
See also Import MSI change port pipelines