For the sake of follow-up: In general, this worked. I had some problems with long file names, so instead of doing this on the desktop, I did it in the C: root, so that the path was as short as possible. This required administrator rights. Also, the process of “repairing” the new, empty .ENL file would cause EndNote to work for about 5 minutes, and then “not responding” according to Windows. I noticed the the .ENL file was then exactly as large (in KB) as the original, so I force-stopped EndNote, and then re-opened it with the new .ENL file. It then had to rebuild using the PDF index (Or something) and that took 10 or 15 minutes. Regardless, it now appears to work.