Effect of installing .NET 4.6 in the build server with existing .NET 4.0

I'm in the situation where I need to install .NET 4.6 in the build server with running web apps targeted to .NET 4.0. Our new web app is targeted to .NET 4.6 so we need to install this version in the build server. But we are worried if this will have a negative effect with the existing application in the server. Note that we're not actually upgrading/migrating those existing applications to .NET 4.6. We just need to install 4.6 so that the newly web app will work in the build server.

We don't want to use 4.0 in our new web application anymore. We targeted to use at least 4.6 version of .NET for our succeeding projects. Any inputs will very much appreciated. Thanks.