Visual Studio not showing all the scripts in the project.

Not sure how but something has gone wrong with Visual Studio and my project. Now when I open Visual Studio a lot of my script files are not there, whole directories full, the project still works, plays and builds, and if I double click the script in Unity it opens in Visual studio but the script is not in the Solution Explorer Window or the Unity Project Explorer. I have tried deleting all the visual studio files and restarting everything but still the scripts do not show up. Is there a way to fix this?