How to get rid of projects added to this solution error after masking a folder

My team has a solution containing several projects. We are using Team Foundation Server in Visual Studio 2013 for version control. I am never really good at two setup projects in a solution, so I thought cloning those folders (In Source Control) would be great, so I don't have to see and deal with them. But when I close these two folders, every time I open this solution, I get a window saying "Projects were recently added to this solution. Do you want to get them from the source?" Whether I choose yes or no, I keep getting this message box every time I open the solution. If I unlock the folders, I will no longer receive this message box. Also, even after masking, projects are still showing up in my Solution Explorer.Has anyone had this problem or knew how to resolve it?