This only happens when I install a reskin: example Trurail Simulations Dash 9 BNSF h1. I have no idea how to prevent this issue from happening. I can however get the engines back.
Sometimes, you need to include what's called a .geopcdx file. If you've already done that, I suggest looking at the cab geo file.,
It helps if you read the instructions with a repaint as they tell you which files need to be copied from where to where.
If you install a repaint it tells you to copy the Geopcdx files from one location to another. When these files don't get copied you only have the couplings showing and no train. The Geopcdx are the Shape files that the repaint is for and without them copied to the new folder it does not work