No there is no way to disable that particular prompt. What we need to figure out is why are you getting that prompt in the first place so we can stop it from happening.
One way is if you have a Test Studio project in Visual Studio then manually delete the .cs/.vb file on disk. The next time you open Visual Studio project, Visual Studio is still going to look for the file. You will get the prompt if this is what you're doing. You should delete the code behind file within Visual Studio instead of using Windows Explorer.
Similarly if you use Test Studio IDE to get rid of a code behind file, then open the Visual Studio project, Visual Studio is still going to look for the code behind file.
Can you determine what set of steps causes the prompt to appear?