this is the part of my mail I did send to my client
May be this will be useful for you whenever you are trying to move your BizTalk Application in the production environment.
Problem :- Most of the BizTalk Applications work when they are installed and tested as an independent application on the box , they will continue to work till someone from other BizTalk application support group comes with a surprising comment that since you installed your application it stopped my application from working.
Reason :-When in enterprise environment we usually reuse couple of .NET assemblies and couple of BizTalk schemas (error reporting schemas) in Orchestrations, which can cause a conflict between two independent applications. BizTalk server gets confused when it comes to two diff. schemas with "same namespace and first tag" combination from two different assemblies.
Proper Approach to make sure this doesn't happen :-
1. Make sure your testing environment has all the application running and working properly similar to Production Server.
2. Then start installing and testing the new application in test environment.
3. Make sure other applications are working along with the new application.
This will give us a confidence level that new application is not going to "stop" your existing working applications on the Production Box.