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Unfortunately, remapping the functions is about the only way to "fix" your PnP decoder. I originally thought you had a wired decoder. In that case, the best way is to swap the motor wires or flip the motor. Flipping the motor may still be possible with your installation but it will require swapping the brass brush contacts as well. Your decision. Lots of work V a little programming. Of course if you are using JMRI, just save that engine as a separate roster entry with its unique settings in case they are needed again.Martin Myers
This situation could only occur if the model was shipped from the factory with a flipped motor (motor contact assembled incorrectly when it was initially assembled). If that was the case, then the model would have ran in the wrong direction (compared to other models on the layout), even in DC mode. I'm not saying that this is impossible, but I have never seen that. I suspect that this would be very rare problem.
No, the OP has RS-2's. I suspect that the PNP decoder is set up to run short hood forward, and he wants to run long-hood forward. When I hard wire a decoder in my RS's "correctly" (orange to bottom brush, gray to top), it runs short hood forward. The NKP ran long hood forward, so usually I just switch the wires. But if you have a PNP decoder, it isn't "wrong" from the factory; it's just that the factory setting is short-hood forward. Combo of CV29 and Function remap fixes things. Write a note if you don't have JMRI (of course, then you'll have to remember where you put the note!).John C.