Just leave it out, don't install anything in that spot.
It won't hurt anything if you do install a 1N4001 there, but it's not necessary.
This was one of the first PCBs I ever made. At the time I had never used a series polarity protection diode so I designed the board to handle series or parallel protection just in case there was an issue (or if I didn't have a Schottky diode on-hand at the time)...