When storing .LINQ files in source control, running them on multiple machines end up checking in minor changes very often, due to the absolute path of relative references also being stored, like this:

<Reference Relative="..\..\MDA.Cards\bin\Debug\MDA.Cards.dll">D:\dev\VS.NET\MtGDeckAnalyzer\MDA.Cards\bin\Debug\MDA.Cards.dll</Reference>

I suggest you don't store the absolute path when you also got the Relative attribute, so that the programs only change when you actually make a change, and not change because you happen to run them on a computer with a different path setup.