I had an issue after upgrading a BizTalk Orchestration project from version 2006r2 to 2010. One of the Orchestrations mysteriously would not open in the Orchestration Editor in Visual Studio. Rather, it would open in the XML editor. The code would compile properly, but obviously this was unacceptable.
I followed these steps and was able to get the Orchestration to open properly in the IDE:
- Close Visual Studio
- Launch the services console with the command: Services.msc. Restart the “Protected Storage” Service (make sure it is in the automatic mode and started).
- Restart IIS with the command : iisreset
- Reset the Visual Studio loaded packages (in a Visual Studio Command Prompt) with the command: devenv.exe /setup /resetskippkgs
After these steps, I right-clicked on the Orchestration in the IDE Solution Explorer, chose “Open With” and then Orchestration Designer just to make sure it would open as expected.
I found this solution here: http://geekswithblogs.net/synBoogaloo/archive/2007/04/17/111745.aspx#423642
John Glisson - Geek of the Cloth 
Thank you very much.. only MS knows why these kinds of errors happen and they dont have blog or place to tell people what to do when these kinds of issues
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I just right-clicked on the orchestration in the Solution Explorer and selected Open With… BizTalk Orchestration Designer (Default).
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I had this problem in VS 2013 + TFS + BizTalk 2013 R2.
My solution was the following: Tools -> Options -> Source Control -> Environment
Uncheck the option “Get everything when a solution or project is opened”
I think this is a bug related with VS 2013 and therefore should be reported to Microsoft!