I could not reproduce your exact problem but I got close. I think there are some implied statements in your process outline that would be critical for us to understand what's really happening. In any case, I think your BizTalk messages do not get overwritten, but that the XmlDocument variables are.
I think you may have been hit by one of the fundamental confusions a developer coming from a Java or VB6 background encounters when working with C#.
C# is a Managed Language
Please, remember that C# is a managed language, in that it uses a garbage collector to reclaim unused references to objects. The key word here is Reference.
When you write the following lines:
xmlDoc2 = "<root><xml/></root>";
SecondMessage = xmlDoc2;
Basically, you have two references to the same content. Namely, two references xmlDoc2 and SecondMessage which refer to the assigned string.
So, depending upon the code you use to "write out" the XML content of your BizTalk messages, you may be overwriting some references.
Furthermore, if this happens in the context of a Construct shape, you may be inadvertently overwriting the content of the BizTalk message itself.
A Solution?
This problem does not usually manifest itself when working with BizTalk. I personally never encountered this issue.
If you update your original question with the exact code for both Expression shapes and the Assignment shape, I'll update this response with more appropriate guidance.