When I wired up my Reprap and started printing, I noticed that all my prints were mirrored along the Y axis — I’d set it up with the end stop at the front and configured it so that the print bed moved forward when I clicked Y- in pronterface (printrun), and not back. (When the table moves back, the print head essentially moves forward along it.)
The end stops were already in place and I didn’t want to move them, but no combination of INVERT_Y_DIR and Y_HOME_DIR in Configuration.h would work. I even tried changing Y_ENDSTOP_INVERT, knowing full well that it wouldn’t help either.
So how do you flip an axis without moving the end stop or the home position? The answer is to change both INVERT_Y_DIR and Y_HOME_DIR in Configuration.h, and also swap the values for Y_MAX_PIN and Y_MIN_PIN in pins.h for the specific motherboard you’re using.