File reference uses assets in an external file, so the first question is whether you have more than one file. If not, then the high res mesh must be in the same file. You say it only shows up during render time? It's possible it's hidden in the viewport, so try checking display layers and fully expand each node in the outliner. Even if it was referenced from an external file, it should be visible in the outliner. If possible, can you show a screenshot of the outliner?