I\'m running into a small but weird annoyance that seems to be happening to other people, too (for example, check out the revision history of SEDE). I have a SQL Server 2008
I believe Visual Studio serializes the dbmdl file every time the project is opened. The only possible work around would be to keep the project open.
If you delete the .dbml file, it is rebuilt without errors or warnings, so I think it's just a cache file for references, intellisense, etc. I'm going to exclude it from source control.
See related question here. The .dbmdl file is unique per user (and some kind of cache, as said above) and so the right solution is indeed to exclude it from source control.