DON"T move the entire runtime folder! There's app specific stuff in there and you'll end up with a mixed version and a real headache. Only move the content folders. (Libraries, Textures, Reflections, Geometries and any Python script you may have.

Once you've moved it out -- leave it out. Just make it a linked runtime and from now on you won't have to worry about overwriting custom content with a re-install.