It was pretty much was unfixable.
I had to delete all the wires from all the views, relink the SCH back up again, and do all the traces in PCB view trusting the ratsnests. But when I came to link the BB view mysterious ratsnests appeared in SCH view. What I think happened was what I said, that you must have done one view and corrected it in another, and because of that previous link the parts went permanently linked and wouldn't clear. I had to duplicate a header and a pot, delete the glitching parts, and put the new ones in. I then trusted the ratsnest in BB view and it cleaned up.
If you did it again doing the SCH view first, because you already had the SCH to copy, and trusted the ratsnests, it probably would have been fine.
Besides the tip of doing only one view first and fixing all errors in that view, you can click on a connection and everything that is connected to it will light up, so you might be able to make shorter connections.
I suggest you do one of the methods I mentioned, because it's good practice, but if you don't want to here is the fixed file.
Ruby2.fzz (958.0 KB)