If you have an IDE with Visual Assist, and then install a new IDE, you must reinstall Visual Assist to make the extension active in the new IDE.
If you install using an executable (.exe) downloaded from wholetomato.com or a Visual Studio Extension (.vsix) downloaded from the Microsoft Visual Studio Gallery, the installer determines which IDEs are installed on your machine, and gives you the option of installing to specific, or all, IDEs. You can re-install Visual Assist to your initial IDE without losing your settings.
If you install using the Extension Manager in Visual Studio 2010 and newer, you can install Visual Assist to your new IDE without affecting the extension in your initial IDE. But, because the Extension Manager requires you to install a new build of Visual Assist from within each IDE, it is easy for builds of Visual Assist within your IDEs to become out of sync using this installation method.