So, I spent all that time setting up the repair data source code, and then discovered that by right-clicking on the layer, going to Data --> Repair Data Source, ArcWhatever fixes all the ones that were in the same folder. Same problem with the base heights though.
Now I'm exporting ArcScene scenes to 2d images. I had originally done this on my laptop and got everything setup on there. There were problems exporting the image with background vector data (roads and coastline). The coastline was a polygon and came out with extra lines cutting across the 3d. So my work around was to export the vector and 3d as separate images and then make them as layers in PhotoShop Elements. This works pretty well. Now I'm working on the desktop and discovered that the images don't export the same size. The reason for this is the monitor size and resolution as the export dimensions are determined by this. You can also change the export dimensions by changing the height and width of ArcScene. This is a pain to duplicate, but at least now I know what the problem is.