If you, like me, have set the GenerateCSFiles property to 1 (as described
here) to get BizTalk to keep the .cs files after they have been generated from the orchestrations and maps, be a bit aware that it
can cause some weird problems sometimes.
I just had one of my orchestrations indicating that there was an error with some of the shapes. The map was missing, seemingly. The odd thing was that the whole solution was compiling correctly, so the problem seemed only to affect the editor.
When looking at the "configure map" settings, the map the shape was referring to had just
disappeared. Yeah, you heard me. It was completely gone. Why? I don't know. The file was located in the project, it was set to Compile on build, but... it didn't work.
The solution: close down Visual Studio. Remove all .cs files from the folder with the orchestration and the folder with the maps. Open the solution, and the problem was gone...