All BizTalk solutions from 2006R2 was upgraded to 2010 version and was checked-in to TFS couple of months back and today I try to get the latest version and tried to compile it and boom! it throws an error.
It seems that when you use the upgrade wizard and try to check-in (TFS), the Assembly.cs file is being ignored.
To solve this I went to the copy of the solution (or History if not available) and copy every Properties folder (which contains the Assembly.cs) to the new one.
Finally in the Source Control, I selected the top folder then click Add Items to the Folder -> Sort it by Name -> Exclude all that is not Assembly.cs -> Finish.
Lesson of the day: to always check whether the Assembly.cs is included during the checkin when migrating a BizTalk solution.